Starting phenix.real_space_refine on Tue Feb 11 19:14:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggc_40002/02_2025/8ggc_40002.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggc_40002/02_2025/8ggc_40002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggc_40002/02_2025/8ggc_40002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggc_40002/02_2025/8ggc_40002.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggc_40002/02_2025/8ggc_40002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggc_40002/02_2025/8ggc_40002.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 38 5.16 5 C 4112 2.51 5 N 1152 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6515 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2123 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 6, 'TRANS': 287} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 205 Chain: "B" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2452 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "G" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 348 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 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: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1545 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 5, 'TRANS': 241} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 616 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 222 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.72 Number of scatterers: 6515 At special positions: 0 Unit cell: (84.1669, 136.229, 98.9178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 3 15.00 O 1210 8.00 N 1152 7.00 C 4112 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: 1.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 46.2% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.570A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.506A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 110 removed outlier: 3.530A pdb=" N LEU A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.634A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 196 through 200 removed outlier: 4.190A pdb=" N CYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 200' Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.830A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.605A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.047A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.604A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.723A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 Processing helix chain 'A' and resid 373 through 383 removed outlier: 4.313A pdb=" N ASN A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 392 removed outlier: 3.835A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.515A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.895A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.938A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.622A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.510A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 55 removed outlier: 3.507A pdb=" N PHE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 95 removed outlier: 3.976A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.877A pdb=" N ALA R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.747A pdb=" N ASP R 113 " --> pdb=" O TRP R 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 172 removed outlier: 3.763A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.999A 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 198 through 208 Processing helix chain 'R' and resid 208 through 235 removed outlier: 3.502A pdb=" N VAL R 216 " --> pdb=" O LEU R 212 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL R 222 " --> pdb=" O VAL R 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 removed outlier: 4.353A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.099A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 316 Processing helix chain 'R' and resid 316 through 322 removed outlier: 4.450A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 213 removed outlier: 3.546A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.741A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.901A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103 removed outlier: 7.028A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.243A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.771A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.480A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.683A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 888 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: 1.86 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1094 1.32 - 1.44: 1819 1.44 - 1.57: 3662 1.57 - 1.69: 6 1.69 - 1.81: 52 Bond restraints: 6633 Sorted by residual: bond pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 1.521 1.446 0.075 1.21e-02 6.83e+03 3.85e+01 bond pdb=" CA TYR A 391 " pdb=" C TYR A 391 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.30e-02 5.92e+03 2.81e+01 bond pdb=" N LEU A 393 " pdb=" CA LEU A 393 " ideal model delta sigma weight residual 1.456 1.397 0.060 1.28e-02 6.10e+03 2.19e+01 bond pdb=" N GLU A 392 " pdb=" CA GLU A 392 " ideal model delta sigma weight residual 1.456 1.413 0.042 1.23e-02 6.61e+03 1.19e+01 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.586 -0.063 2.00e-02 2.50e+03 9.88e+00 ... (remaining 6628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 8901 2.32 - 4.64: 127 4.64 - 6.96: 22 6.96 - 9.27: 11 9.27 - 11.59: 7 Bond angle restraints: 9068 Sorted by residual: angle pdb=" N GLN A 390 " pdb=" CA GLN A 390 " pdb=" C GLN A 390 " ideal model delta sigma weight residual 111.28 121.54 -10.26 1.09e+00 8.42e-01 8.85e+01 angle pdb=" N LEU A 393 " pdb=" CA LEU A 393 " pdb=" C LEU A 393 " ideal model delta sigma weight residual 110.10 98.51 11.59 1.49e+00 4.50e-01 6.05e+01 angle pdb=" N GLU A 392 " pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 108.79 99.59 9.20 1.53e+00 4.27e-01 3.62e+01 angle pdb=" N PRO R 138 " pdb=" CA PRO R 138 " pdb=" C PRO R 138 " ideal model delta sigma weight residual 113.53 121.74 -8.21 1.39e+00 5.18e-01 3.49e+01 angle pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta sigma weight residual 122.68 114.35 8.33 1.47e+00 4.63e-01 3.21e+01 ... (remaining 9063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.35: 3751 29.35 - 58.71: 95 58.71 - 88.06: 5 88.06 - 117.42: 4 117.42 - 146.77: 2 Dihedral angle restraints: 3857 sinusoidal: 1143 harmonic: 2714 Sorted by residual: dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 157.02 146.77 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -15.68 120.28 1 2.00e+01 2.50e-03 3.61e+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 260.87 146.58 114.29 1 2.00e+01 2.50e-03 3.39e+01 ... (remaining 3854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 876 0.055 - 0.109: 165 0.109 - 0.164: 27 0.164 - 0.219: 9 0.219 - 0.273: 3 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CA GLU A 230 " pdb=" N GLU A 230 " pdb=" C GLU A 230 " pdb=" CB GLU A 230 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA VAL A 224 " pdb=" N VAL A 224 " pdb=" C VAL A 224 " pdb=" CB VAL A 224 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PRO R 138 " pdb=" N PRO R 138 " pdb=" C PRO R 138 " pdb=" CB PRO R 138 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1077 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 223 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C ASP A 223 " 0.066 2.00e-02 2.50e+03 pdb=" O ASP A 223 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 224 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 225 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C GLY A 225 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY A 225 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 226 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 324 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C ALA A 324 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA A 324 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 325 " -0.013 2.00e-02 2.50e+03 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1456 2.78 - 3.31: 5922 3.31 - 3.84: 9808 3.84 - 4.37: 10609 4.37 - 4.90: 19403 Nonbonded interactions: 47198 Sorted by model distance: nonbonded pdb=" CD1 ILE A 207 " pdb=" O ASP A 223 " model vdw 2.250 3.460 nonbonded pdb=" O CYS A 162 " pdb=" OH TYR A 169 " model vdw 2.290 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.293 3.040 nonbonded pdb=" OG SER B 97 " pdb=" OD2 ASP B 118 " model vdw 2.299 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.315 3.040 ... (remaining 47193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.520 Find NCS groups from input model: 0.080 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 0.075 6633 Z= 0.277 Angle : 0.731 11.592 9068 Z= 0.424 Chirality : 0.046 0.273 1080 Planarity : 0.004 0.040 1167 Dihedral : 14.244 146.773 2087 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.19 % Allowed : 1.12 % Favored : 98.69 % 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: 904 helix: 1.58 (0.26), residues: 377 sheet: -0.76 (0.41), residues: 176 loop : -1.36 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 99 HIS 0.004 0.001 HIS A 387 PHE 0.011 0.001 PHE A 208 TYR 0.016 0.001 TYR R 316 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.742 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.1755 time to fit residues: 22.7345 Evaluate side-chains 82 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 46 optimal weight: 0.0010 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117811 restraints weight = 9998.838| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.66 r_work: 0.3463 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6633 Z= 0.252 Angle : 0.525 8.014 9068 Z= 0.283 Chirality : 0.043 0.162 1080 Planarity : 0.003 0.035 1167 Dihedral : 8.829 131.796 1011 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.12 % Allowed : 9.74 % Favored : 89.14 % 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: 0.49 (0.29), residues: 904 helix: 2.06 (0.26), residues: 398 sheet: -0.63 (0.44), residues: 165 loop : -1.30 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.011 0.001 HIS B 142 PHE 0.017 0.002 PHE A 290 TYR 0.013 0.001 TYR A 360 ARG 0.008 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.744 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 94 average time/residue: 0.1448 time to fit residues: 19.5136 Evaluate side-chains 83 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 167 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 213 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 220 GLN R 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.150127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112390 restraints weight = 9957.957| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.63 r_work: 0.3349 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6633 Z= 0.246 Angle : 0.502 8.387 9068 Z= 0.267 Chirality : 0.042 0.148 1080 Planarity : 0.003 0.037 1167 Dihedral : 8.188 112.537 1009 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.06 % Allowed : 14.79 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.29), residues: 904 helix: 2.20 (0.26), residues: 397 sheet: -0.59 (0.43), residues: 164 loop : -1.26 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 99 HIS 0.009 0.002 HIS B 142 PHE 0.016 0.002 PHE A 376 TYR 0.014 0.001 TYR A 360 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.690 Fit side-chains REVERT: A 209 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8139 (mt-10) REVERT: R 212 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6384 (mp) outliers start: 11 outliers final: 5 residues processed: 84 average time/residue: 0.1526 time to fit residues: 18.3184 Evaluate side-chains 76 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 61 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 68 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 142 HIS R 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115227 restraints weight = 9855.478| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.67 r_work: 0.3390 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6633 Z= 0.140 Angle : 0.448 8.522 9068 Z= 0.235 Chirality : 0.040 0.134 1080 Planarity : 0.003 0.034 1167 Dihedral : 7.503 107.968 1009 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.50 % Allowed : 17.98 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.29), residues: 904 helix: 2.35 (0.27), residues: 399 sheet: -0.69 (0.42), residues: 167 loop : -1.21 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.005 0.001 HIS B 142 PHE 0.015 0.001 PHE A 376 TYR 0.012 0.001 TYR A 360 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.709 Fit side-chains REVERT: G 18 GLN cc_start: 0.8891 (tt0) cc_final: 0.8641 (tt0) outliers start: 8 outliers final: 7 residues processed: 91 average time/residue: 0.1623 time to fit residues: 20.6968 Evaluate side-chains 88 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 127 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.150909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113245 restraints weight = 9913.207| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.65 r_work: 0.3360 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6633 Z= 0.216 Angle : 0.483 8.885 9068 Z= 0.254 Chirality : 0.042 0.141 1080 Planarity : 0.003 0.036 1167 Dihedral : 7.376 107.062 1009 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.81 % Allowed : 18.35 % Favored : 78.84 % 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: 0.74 (0.29), residues: 904 helix: 2.41 (0.27), residues: 398 sheet: -0.70 (0.42), residues: 167 loop : -1.26 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.013 0.001 HIS B 142 PHE 0.016 0.001 PHE B 241 TYR 0.012 0.001 TYR A 360 ARG 0.007 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.694 Fit side-chains REVERT: A 209 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8052 (mt-10) REVERT: G 18 GLN cc_start: 0.8941 (tt0) cc_final: 0.8675 (tt0) REVERT: R 229 GLN cc_start: 0.6494 (tp-100) cc_final: 0.6288 (tp-100) outliers start: 15 outliers final: 11 residues processed: 88 average time/residue: 0.1670 time to fit residues: 20.4187 Evaluate side-chains 87 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 60 optimal weight: 1.9990 chunk 83 optimal weight: 0.0570 chunk 74 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 overall best weight: 1.0504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.150769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113072 restraints weight = 9891.298| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.67 r_work: 0.3360 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6633 Z= 0.195 Angle : 0.482 8.914 9068 Z= 0.252 Chirality : 0.041 0.131 1080 Planarity : 0.003 0.037 1167 Dihedral : 7.236 105.486 1009 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.18 % Allowed : 18.73 % Favored : 78.09 % 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: 0.78 (0.29), residues: 904 helix: 2.44 (0.27), residues: 398 sheet: -0.65 (0.42), residues: 165 loop : -1.24 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.009 0.001 HIS B 142 PHE 0.016 0.001 PHE A 376 TYR 0.011 0.001 TYR A 360 ARG 0.007 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.752 Fit side-chains REVERT: B 258 ASP cc_start: 0.7178 (t70) cc_final: 0.6450 (t0) REVERT: G 18 GLN cc_start: 0.8958 (tt0) cc_final: 0.8726 (tt0) REVERT: R 229 GLN cc_start: 0.6510 (tp-100) cc_final: 0.6268 (tp-100) outliers start: 17 outliers final: 13 residues processed: 89 average time/residue: 0.1733 time to fit residues: 21.2858 Evaluate side-chains 90 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 88 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113547 restraints weight = 9950.034| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.68 r_work: 0.3386 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6633 Z= 0.174 Angle : 0.474 8.711 9068 Z= 0.246 Chirality : 0.041 0.138 1080 Planarity : 0.003 0.037 1167 Dihedral : 7.065 104.070 1009 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.00 % Allowed : 18.91 % Favored : 78.09 % 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: 0.78 (0.29), residues: 904 helix: 2.45 (0.27), residues: 399 sheet: -0.66 (0.42), residues: 165 loop : -1.27 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.008 0.001 HIS B 142 PHE 0.015 0.001 PHE A 376 TYR 0.011 0.001 TYR A 360 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.787 Fit side-chains REVERT: B 142 HIS cc_start: 0.5897 (OUTLIER) cc_final: 0.5061 (m170) REVERT: B 258 ASP cc_start: 0.7253 (t70) cc_final: 0.6538 (t0) REVERT: G 18 GLN cc_start: 0.8941 (tt0) cc_final: 0.8723 (tt0) outliers start: 16 outliers final: 13 residues processed: 90 average time/residue: 0.1616 time to fit residues: 20.3014 Evaluate side-chains 88 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.151195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113502 restraints weight = 9828.024| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.66 r_work: 0.3377 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6633 Z= 0.172 Angle : 0.478 8.646 9068 Z= 0.248 Chirality : 0.041 0.132 1080 Planarity : 0.003 0.038 1167 Dihedral : 6.896 102.880 1009 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.81 % Allowed : 19.48 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 904 helix: 2.49 (0.27), residues: 399 sheet: -0.62 (0.42), residues: 165 loop : -1.27 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 169 HIS 0.012 0.001 HIS B 142 PHE 0.015 0.001 PHE A 376 TYR 0.011 0.001 TYR A 360 ARG 0.006 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.720 Fit side-chains REVERT: B 258 ASP cc_start: 0.7228 (t70) cc_final: 0.6517 (t0) REVERT: G 18 GLN cc_start: 0.8952 (tt0) cc_final: 0.8744 (tt0) REVERT: R 229 GLN cc_start: 0.6554 (tp-100) cc_final: 0.6303 (tp-100) outliers start: 15 outliers final: 13 residues processed: 85 average time/residue: 0.1666 time to fit residues: 19.7885 Evaluate side-chains 86 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 44 optimal weight: 0.0980 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 0.0980 chunk 50 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.154025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116238 restraints weight = 9964.566| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.69 r_work: 0.3403 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6633 Z= 0.107 Angle : 0.445 7.541 9068 Z= 0.229 Chirality : 0.040 0.138 1080 Planarity : 0.003 0.037 1167 Dihedral : 6.394 99.548 1009 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.50 % Allowed : 21.16 % Favored : 77.34 % 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: 0.91 (0.29), residues: 904 helix: 2.60 (0.27), residues: 401 sheet: -0.61 (0.42), residues: 162 loop : -1.28 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.008 0.001 HIS B 142 PHE 0.015 0.001 PHE R 208 TYR 0.010 0.001 TYR A 360 ARG 0.007 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.719 Fit side-chains REVERT: B 258 ASP cc_start: 0.7126 (t70) cc_final: 0.6586 (t0) REVERT: G 18 GLN cc_start: 0.8948 (tt0) cc_final: 0.8535 (pt0) outliers start: 8 outliers final: 5 residues processed: 88 average time/residue: 0.1650 time to fit residues: 20.2541 Evaluate side-chains 83 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 73 optimal weight: 0.2980 chunk 85 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.0010 chunk 67 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 chunk 10 optimal weight: 0.0370 chunk 35 optimal weight: 0.5980 overall best weight: 0.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 142 HIS R 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122132 restraints weight = 10076.999| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.73 r_work: 0.3518 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6633 Z= 0.102 Angle : 0.453 8.760 9068 Z= 0.232 Chirality : 0.040 0.161 1080 Planarity : 0.003 0.036 1167 Dihedral : 5.958 96.430 1009 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.50 % Allowed : 20.97 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 904 helix: 2.68 (0.27), residues: 400 sheet: -0.26 (0.45), residues: 150 loop : -1.29 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.000 HIS B 142 PHE 0.013 0.001 PHE A 376 TYR 0.010 0.001 TYR A 360 ARG 0.008 0.000 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.664 Fit side-chains REVERT: B 151 PHE cc_start: 0.8354 (m-10) cc_final: 0.8093 (m-80) REVERT: B 258 ASP cc_start: 0.6967 (t70) cc_final: 0.6517 (t0) REVERT: G 18 GLN cc_start: 0.8896 (tt0) cc_final: 0.8556 (pt0) outliers start: 8 outliers final: 8 residues processed: 87 average time/residue: 0.1606 time to fit residues: 19.7585 Evaluate side-chains 81 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.156941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119043 restraints weight = 10218.439| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.74 r_work: 0.3465 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6633 Z= 0.169 Angle : 0.475 8.856 9068 Z= 0.243 Chirality : 0.041 0.155 1080 Planarity : 0.003 0.038 1167 Dihedral : 6.041 97.568 1009 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.31 % Allowed : 21.91 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.29), residues: 904 helix: 2.73 (0.27), residues: 400 sheet: -0.63 (0.43), residues: 162 loop : -1.18 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.010 0.001 HIS B 142 PHE 0.015 0.001 PHE B 241 TYR 0.012 0.001 TYR A 360 ARG 0.008 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3461.38 seconds wall clock time: 61 minutes 58.95 seconds (3718.95 seconds total)