Starting phenix.real_space_refine on Fri Aug 22 16:14:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uo4_42427/08_2025/8uo4_42427.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uo4_42427/08_2025/8uo4_42427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uo4_42427/08_2025/8uo4_42427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uo4_42427/08_2025/8uo4_42427.map" model { file = "/net/cci-nas-00/data/ceres_data/8uo4_42427/08_2025/8uo4_42427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uo4_42427/08_2025/8uo4_42427.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.015 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 16 5.16 5 C 3576 2.51 5 N 1034 2.21 5 O 1072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5702 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 1854 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 7, 'TRANS': 284} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 610 Unresolved non-hydrogen angles: 758 Unresolved non-hydrogen dihedrals: 495 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLU:plan': 27, 'ASP:plan': 13, 'GLN:plan1': 10, 'ARG:plan': 21, 'ASN:plan1': 10, 'HIS:plan': 3, 'PHE:plan': 3, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 392 Chain: "B" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2224 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 282 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 20, 'GLN:plan1': 8, 'ARG:plan': 12, 'ASN:plan1': 11, 'TYR:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 241 Chain: "G" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 307 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "R" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1269 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 809 Unresolved non-hydrogen dihedrals: 514 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'PHE:plan': 15, 'ASN:plan1': 10, 'GLN:plan1': 6, 'TYR:plan': 5, 'ASP:plan': 5, 'HIS:plan': 4, 'TRP:plan': 5, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 309 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 1.32, per 1000 atoms: 0.23 Number of scatterers: 5702 At special positions: 0 Unit cell: (85.0346, 137.097, 100.653, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 P 3 15.00 Mg 1 11.99 O 1072 8.00 N 1034 7.00 C 3576 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 276.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1732 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 44.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 9 through 40 removed outlier: 3.915A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 65 removed outlier: 3.813A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.601A pdb=" N ASN A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 157 removed outlier: 3.505A pdb=" N ALA A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.825A pdb=" N GLU A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.561A pdb=" N ASN A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.866A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.643A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.906A pdb=" N HIS A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 4.189A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 32 through 44 Processing helix chain 'R' and resid 36 through 55 removed outlier: 3.744A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 91 removed outlier: 3.853A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.509A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 171 removed outlier: 3.569A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.709A 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 184 removed outlier: 3.927A pdb=" N ASN R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 179 through 184' Processing helix chain 'R' and resid 198 through 208 Processing helix chain 'R' and resid 209 through 234 removed outlier: 4.092A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 296 removed outlier: 4.040A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.962A pdb=" N HIS R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 326 removed outlier: 3.566A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU R 310 " --> pdb=" O GLU R 306 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU R 311 " --> pdb=" O VAL R 307 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN R 312 " --> pdb=" O TYR R 308 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 212 removed outlier: 3.531A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.207A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.778A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.947A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.493A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.268A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.615A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 858 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: 0.73 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1959 1.34 - 1.46: 1163 1.46 - 1.58: 2638 1.58 - 1.69: 5 1.69 - 1.81: 20 Bond restraints: 5785 Sorted by residual: bond pdb=" N ILE A 383 " pdb=" CA ILE A 383 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.09e-02 8.42e+03 1.27e+01 bond pdb=" N TYR A 391 " pdb=" CA TYR A 391 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 7.00e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" N MET A 386 " pdb=" CA MET A 386 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.16e+00 bond pdb=" N ARG A 380 " pdb=" CA ARG A 380 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.06e+00 ... (remaining 5780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 7886 2.96 - 5.93: 62 5.93 - 8.89: 11 8.89 - 11.86: 4 11.86 - 14.82: 1 Bond angle restraints: 7964 Sorted by residual: angle pdb=" N ILE A 383 " pdb=" CA ILE A 383 " pdb=" C ILE A 383 " ideal model delta sigma weight residual 111.88 102.30 9.58 1.06e+00 8.90e-01 8.17e+01 angle pdb=" N ASN A 377 " pdb=" CA ASN A 377 " pdb=" C ASN A 377 " ideal model delta sigma weight residual 111.71 105.31 6.40 1.15e+00 7.56e-01 3.09e+01 angle pdb=" PB GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sigma weight residual 120.50 135.32 -14.82 3.00e+00 1.11e-01 2.44e+01 angle pdb=" CA GLN A 390 " pdb=" C GLN A 390 " pdb=" O GLN A 390 " ideal model delta sigma weight residual 121.84 116.75 5.09 1.16e+00 7.43e-01 1.92e+01 angle pdb=" N GLU A 392 " pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 109.96 103.66 6.30 1.49e+00 4.50e-01 1.79e+01 ... (remaining 7959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.19: 3274 29.19 - 58.39: 51 58.39 - 87.58: 3 87.58 - 116.77: 1 116.77 - 145.97: 1 Dihedral angle restraints: 3330 sinusoidal: 687 harmonic: 2643 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 -41.37 145.97 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 150.85 110.02 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" CA CYS A 237 " pdb=" C CYS A 237 " pdb=" N PHE A 238 " pdb=" CA PHE A 238 " ideal model delta harmonic sigma weight residual 180.00 162.73 17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 3327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 883 0.067 - 0.133: 100 0.133 - 0.200: 5 0.200 - 0.266: 3 0.266 - 0.333: 1 Chirality restraints: 992 Sorted by residual: chirality pdb=" CA ILE A 383 " pdb=" N ILE A 383 " pdb=" C ILE A 383 " pdb=" CB ILE A 383 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.77e+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 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 382 " pdb=" N ILE A 382 " pdb=" C ILE A 382 " pdb=" CB ILE A 382 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 989 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 376 " 0.012 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" C PHE A 376 " -0.044 2.00e-02 2.50e+03 pdb=" O PHE A 376 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 377 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 382 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C ILE A 382 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 382 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 383 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO G 49 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.021 5.00e-02 4.00e+02 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2040 2.84 - 3.35: 5330 3.35 - 3.87: 8398 3.87 - 4.38: 8555 4.38 - 4.90: 14978 Nonbonded interactions: 39301 Sorted by model distance: nonbonded pdb=" O SER G 31 " pdb=" OG SER G 31 " model vdw 2.322 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A 54 " pdb=" OD2 ASP A 223 " model vdw 2.369 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.371 3.040 nonbonded pdb=" O GLY B 141 " pdb=" NE2 GLN B 176 " model vdw 2.374 3.120 ... (remaining 39296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.720 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 0.052 5785 Z= 0.224 Angle : 0.716 14.824 7964 Z= 0.406 Chirality : 0.045 0.333 992 Planarity : 0.003 0.037 1040 Dihedral : 11.999 145.967 1598 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.29), residues: 870 helix: 1.82 (0.28), residues: 353 sheet: -1.40 (0.42), residues: 159 loop : -1.25 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 317 TYR 0.005 0.001 TYR B 105 PHE 0.012 0.001 PHE B 235 TRP 0.011 0.001 TRP A 234 HIS 0.006 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 5785) covalent geometry : angle 0.71608 ( 7964) hydrogen bonds : bond 0.26051 ( 291) hydrogen bonds : angle 7.00757 ( 858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0474 time to fit residues: 5.6586 Evaluate side-chains 58 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091146 restraints weight = 16599.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.090789 restraints weight = 13834.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092019 restraints weight = 11824.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.092081 restraints weight = 9192.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.092411 restraints weight = 8486.199| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 5785 Z= 0.146 Angle : 0.514 7.091 7964 Z= 0.284 Chirality : 0.041 0.155 992 Planarity : 0.003 0.035 1040 Dihedral : 7.045 139.776 958 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.44 % Allowed : 10.06 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.29), residues: 870 helix: 1.59 (0.27), residues: 381 sheet: -1.23 (0.41), residues: 165 loop : -1.33 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.017 0.001 TYR B 124 PHE 0.010 0.001 PHE B 292 TRP 0.013 0.001 TRP A 277 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5785) covalent geometry : angle 0.51423 ( 7964) hydrogen bonds : bond 0.04908 ( 291) hydrogen bonds : angle 4.97475 ( 858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.227 Fit side-chains REVERT: B 339 TRP cc_start: 0.8657 (OUTLIER) cc_final: 0.8316 (m-10) REVERT: G 41 CYS cc_start: 0.8109 (m) cc_final: 0.7626 (p) outliers start: 8 outliers final: 7 residues processed: 63 average time/residue: 0.0299 time to fit residues: 3.2275 Evaluate side-chains 66 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 64 optimal weight: 0.0270 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 79 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.094205 restraints weight = 16295.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093683 restraints weight = 13176.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094471 restraints weight = 11987.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094719 restraints weight = 9911.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095188 restraints weight = 8691.264| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5785 Z= 0.088 Angle : 0.442 6.679 7964 Z= 0.239 Chirality : 0.040 0.130 992 Planarity : 0.003 0.032 1040 Dihedral : 6.376 130.167 958 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.13 % Allowed : 11.89 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.29), residues: 870 helix: 2.04 (0.28), residues: 375 sheet: -1.15 (0.41), residues: 165 loop : -1.20 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.015 0.001 TYR B 124 PHE 0.008 0.001 PHE B 292 TRP 0.024 0.002 TRP A 234 HIS 0.008 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 5785) covalent geometry : angle 0.44170 ( 7964) hydrogen bonds : bond 0.03256 ( 291) hydrogen bonds : angle 3.94432 ( 858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.181 Fit side-chains REVERT: B 234 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: B 339 TRP cc_start: 0.8448 (m100) cc_final: 0.7975 (m-10) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.0376 time to fit residues: 4.4684 Evaluate side-chains 65 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 11 optimal weight: 0.0050 chunk 29 optimal weight: 30.0000 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 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 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094005 restraints weight = 16307.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093618 restraints weight = 13439.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094372 restraints weight = 11995.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094563 restraints weight = 10119.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095278 restraints weight = 8785.328| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5785 Z= 0.081 Angle : 0.421 6.415 7964 Z= 0.226 Chirality : 0.039 0.128 992 Planarity : 0.003 0.032 1040 Dihedral : 6.081 124.249 958 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.44 % Allowed : 14.02 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.29), residues: 870 helix: 2.15 (0.27), residues: 382 sheet: -0.94 (0.40), residues: 175 loop : -1.20 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.010 0.001 TYR B 124 PHE 0.007 0.001 PHE A 212 TRP 0.017 0.001 TRP B 297 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00166 ( 5785) covalent geometry : angle 0.42110 ( 7964) hydrogen bonds : bond 0.02779 ( 291) hydrogen bonds : angle 3.67926 ( 858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.199 Fit side-chains REVERT: B 234 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: B 339 TRP cc_start: 0.8507 (m100) cc_final: 0.8143 (m-10) outliers start: 8 outliers final: 6 residues processed: 71 average time/residue: 0.0309 time to fit residues: 3.6017 Evaluate side-chains 68 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 57 optimal weight: 0.0970 chunk 72 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 overall best weight: 1.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.109378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.091999 restraints weight = 16604.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.091537 restraints weight = 13769.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092738 restraints weight = 12057.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.092772 restraints weight = 9364.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.093122 restraints weight = 8721.676| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5785 Z= 0.118 Angle : 0.447 6.119 7964 Z= 0.243 Chirality : 0.040 0.128 992 Planarity : 0.003 0.033 1040 Dihedral : 6.049 121.802 958 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.57 % Allowed : 15.24 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.29), residues: 870 helix: 2.19 (0.27), residues: 382 sheet: -0.92 (0.40), residues: 174 loop : -1.20 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 347 TYR 0.008 0.001 TYR A 360 PHE 0.009 0.001 PHE B 235 TRP 0.022 0.002 TRP B 297 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5785) covalent geometry : angle 0.44723 ( 7964) hydrogen bonds : bond 0.03275 ( 291) hydrogen bonds : angle 3.76966 ( 858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.239 Fit side-chains REVERT: B 234 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: B 339 TRP cc_start: 0.8560 (m100) cc_final: 0.8108 (m-10) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.0353 time to fit residues: 4.0725 Evaluate side-chains 71 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.111170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093788 restraints weight = 16351.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.093402 restraints weight = 13503.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094577 restraints weight = 11948.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094654 restraints weight = 9163.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094991 restraints weight = 8568.959| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5785 Z= 0.080 Angle : 0.424 6.131 7964 Z= 0.226 Chirality : 0.039 0.130 992 Planarity : 0.003 0.031 1040 Dihedral : 5.794 117.100 958 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.35 % Allowed : 15.55 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.29), residues: 870 helix: 2.32 (0.27), residues: 382 sheet: -0.91 (0.40), residues: 176 loop : -1.17 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.004 0.001 TYR A 311 PHE 0.008 0.001 PHE A 212 TRP 0.020 0.001 TRP A 234 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00165 ( 5785) covalent geometry : angle 0.42365 ( 7964) hydrogen bonds : bond 0.02652 ( 291) hydrogen bonds : angle 3.54819 ( 858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.209 Fit side-chains REVERT: A 234 TRP cc_start: 0.8358 (p90) cc_final: 0.8124 (p-90) REVERT: B 234 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: B 339 TRP cc_start: 0.8551 (m100) cc_final: 0.8082 (m-10) outliers start: 11 outliers final: 7 residues processed: 71 average time/residue: 0.0340 time to fit residues: 3.9988 Evaluate side-chains 71 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.0570 chunk 70 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.6904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.107700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.090282 restraints weight = 16560.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090135 restraints weight = 14373.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.091187 restraints weight = 12518.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091278 restraints weight = 9736.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.091541 restraints weight = 9104.255| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5785 Z= 0.147 Angle : 0.488 5.841 7964 Z= 0.263 Chirality : 0.041 0.141 992 Planarity : 0.003 0.035 1040 Dihedral : 5.997 116.562 958 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.88 % Allowed : 15.24 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.29), residues: 870 helix: 2.16 (0.27), residues: 382 sheet: -1.01 (0.41), residues: 166 loop : -1.27 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.011 0.001 TYR A 360 PHE 0.013 0.001 PHE B 235 TRP 0.030 0.002 TRP B 297 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5785) covalent geometry : angle 0.48817 ( 7964) hydrogen bonds : bond 0.03661 ( 291) hydrogen bonds : angle 3.90025 ( 858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.211 Fit side-chains REVERT: A 234 TRP cc_start: 0.8441 (p90) cc_final: 0.8236 (p-90) REVERT: B 234 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: B 339 TRP cc_start: 0.8619 (m100) cc_final: 0.8030 (m-10) outliers start: 16 outliers final: 13 residues processed: 68 average time/residue: 0.0362 time to fit residues: 4.0812 Evaluate side-chains 72 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 30.0000 chunk 42 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.108617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.091119 restraints weight = 16292.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090829 restraints weight = 13211.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.091926 restraints weight = 11675.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092011 restraints weight = 9128.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.092257 restraints weight = 8480.086| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5785 Z= 0.115 Angle : 0.458 5.859 7964 Z= 0.246 Chirality : 0.040 0.136 992 Planarity : 0.003 0.034 1040 Dihedral : 5.891 115.097 958 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.27 % Allowed : 16.46 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.29), residues: 870 helix: 2.27 (0.27), residues: 380 sheet: -1.11 (0.40), residues: 169 loop : -1.30 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.008 0.001 TYR A 360 PHE 0.010 0.001 PHE B 292 TRP 0.018 0.001 TRP B 297 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5785) covalent geometry : angle 0.45840 ( 7964) hydrogen bonds : bond 0.03233 ( 291) hydrogen bonds : angle 3.77612 ( 858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.144 Fit side-chains REVERT: A 234 TRP cc_start: 0.8447 (p90) cc_final: 0.8181 (p-90) REVERT: B 234 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: B 339 TRP cc_start: 0.8609 (m100) cc_final: 0.7991 (m-10) outliers start: 14 outliers final: 11 residues processed: 67 average time/residue: 0.0348 time to fit residues: 3.8509 Evaluate side-chains 70 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 85 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.0060 chunk 89 optimal weight: 10.0000 chunk 11 optimal weight: 0.0020 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 0.0060 chunk 54 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 overall best weight: 0.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.111223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093720 restraints weight = 16266.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.093563 restraints weight = 13018.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094657 restraints weight = 11511.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094724 restraints weight = 8846.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.095146 restraints weight = 8122.436| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5785 Z= 0.077 Angle : 0.428 6.047 7964 Z= 0.228 Chirality : 0.039 0.129 992 Planarity : 0.002 0.031 1040 Dihedral : 5.557 109.851 958 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.66 % Allowed : 16.77 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.30), residues: 870 helix: 2.39 (0.27), residues: 381 sheet: -0.99 (0.41), residues: 171 loop : -1.17 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.004 0.000 TYR G 40 PHE 0.009 0.001 PHE A 222 TRP 0.011 0.001 TRP A 277 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00154 ( 5785) covalent geometry : angle 0.42848 ( 7964) hydrogen bonds : bond 0.02481 ( 291) hydrogen bonds : angle 3.50757 ( 858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.139 Fit side-chains REVERT: A 234 TRP cc_start: 0.8447 (p90) cc_final: 0.8185 (p-90) REVERT: B 234 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 339 TRP cc_start: 0.8568 (m100) cc_final: 0.7935 (m-10) outliers start: 12 outliers final: 5 residues processed: 74 average time/residue: 0.0351 time to fit residues: 4.0409 Evaluate side-chains 70 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.110418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093190 restraints weight = 16347.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.093072 restraints weight = 12698.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.094017 restraints weight = 11396.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.094127 restraints weight = 8912.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.094424 restraints weight = 8189.155| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5785 Z= 0.086 Angle : 0.443 6.033 7964 Z= 0.234 Chirality : 0.039 0.133 992 Planarity : 0.002 0.031 1040 Dihedral : 5.442 106.924 958 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.44 % Allowed : 17.99 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.30), residues: 870 helix: 2.46 (0.27), residues: 381 sheet: -0.97 (0.40), residues: 176 loop : -1.17 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 304 TYR 0.008 0.001 TYR B 59 PHE 0.009 0.001 PHE B 292 TRP 0.021 0.001 TRP B 297 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00184 ( 5785) covalent geometry : angle 0.44258 ( 7964) hydrogen bonds : bond 0.02571 ( 291) hydrogen bonds : angle 3.44362 ( 858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.174 Fit side-chains REVERT: A 234 TRP cc_start: 0.8476 (p90) cc_final: 0.8221 (p-90) REVERT: B 61 MET cc_start: 0.9029 (ppp) cc_final: 0.8330 (ppp) REVERT: B 82 TRP cc_start: 0.8730 (m100) cc_final: 0.8512 (m-10) REVERT: B 234 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: B 339 TRP cc_start: 0.8544 (m100) cc_final: 0.7964 (m-10) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.0383 time to fit residues: 4.1575 Evaluate side-chains 71 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.0670 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN R 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.092837 restraints weight = 15908.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092858 restraints weight = 12040.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.093656 restraints weight = 10490.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093735 restraints weight = 8846.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.094091 restraints weight = 7799.424| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5785 Z= 0.100 Angle : 0.447 5.992 7964 Z= 0.238 Chirality : 0.039 0.132 992 Planarity : 0.003 0.031 1040 Dihedral : 5.438 106.420 958 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.74 % Allowed : 18.29 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.30), residues: 870 helix: 2.42 (0.27), residues: 381 sheet: -1.02 (0.40), residues: 176 loop : -1.18 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 304 TYR 0.005 0.001 TYR A 360 PHE 0.008 0.001 PHE A 222 TRP 0.015 0.001 TRP B 297 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 5785) covalent geometry : angle 0.44724 ( 7964) hydrogen bonds : bond 0.02795 ( 291) hydrogen bonds : angle 3.42841 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 888.40 seconds wall clock time: 15 minutes 55.41 seconds (955.41 seconds total)