Starting phenix.real_space_refine on Wed Jan 15 14:50:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xve_38702/01_2025/8xve_38702.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xve_38702/01_2025/8xve_38702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xve_38702/01_2025/8xve_38702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xve_38702/01_2025/8xve_38702.map" model { file = "/net/cci-nas-00/data/ceres_data/8xve_38702/01_2025/8xve_38702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xve_38702/01_2025/8xve_38702.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5421 2.51 5 N 1474 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8524 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1943 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 430 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 131 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "R" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2459 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.28, per 1000 atoms: 0.62 Number of scatterers: 8524 At special positions: 0 Unit cell: (82.16, 101.92, 146.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1571 8.00 N 1474 7.00 C 5421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.04 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.04 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: 2.06 Conformation dependent library (CDL) restraints added in 1.0 seconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2034 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 44.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 9 through 40 Processing helix chain 'A' and resid 52 through 63 removed outlier: 4.155A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.596A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 302 through 308 removed outlier: 3.537A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 342 removed outlier: 3.739A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.778A pdb=" N LYS B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 13 removed outlier: 4.332A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 25 removed outlier: 4.019A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.531A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 8 through 18 removed outlier: 3.545A pdb=" N VAL P 12 " --> pdb=" O ASP P 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 129 removed outlier: 3.796A pdb=" N ASN R 129 " --> pdb=" O ILE R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 133 Processing helix chain 'R' and resid 134 through 153 removed outlier: 3.828A pdb=" N LEU R 139 " --> pdb=" O GLY R 135 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE R 140 " --> pdb=" O PRO R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 165 removed outlier: 3.795A pdb=" N LEU R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 175 removed outlier: 4.374A pdb=" N MET R 173 " --> pdb=" O PHE R 169 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS R 175 " --> pdb=" O ALA R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 205 Processing helix chain 'R' and resid 215 through 239 removed outlier: 3.565A pdb=" N VAL R 223 " --> pdb=" O ALA R 219 " (cutoff:3.500A) Proline residue: R 235 - end of helix Processing helix chain 'R' and resid 263 through 281 removed outlier: 5.705A pdb=" N ASP R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TRP R 275 " --> pdb=" O THR R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 302 removed outlier: 3.800A pdb=" N PHE R 292 " --> pdb=" O ILE R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 350 Proline residue: R 338 - end of helix removed outlier: 3.542A pdb=" N TYR R 350 " --> pdb=" O LYS R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 390 removed outlier: 3.692A pdb=" N ASN R 373 " --> pdb=" O TYR R 369 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER R 379 " --> pdb=" O ALA R 375 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 390 through 398 removed outlier: 4.813A pdb=" N CYS R 396 " --> pdb=" O ARG R 392 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS R 398 " --> pdb=" O LYS R 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 3.837A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.489A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.562A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.755A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.506A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.827A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.624A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.812A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 6.100A pdb=" N GLY N 16 " --> pdb=" O SER N 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.776A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 240 through 247 454 hydrogen bonds defined for protein. 1296 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: 2.37 Time building geometry restraints manager: 2.39 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: 2777 1.34 - 1.46: 1761 1.46 - 1.58: 4079 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 8697 Sorted by residual: bond pdb=" N ASP B 298 " pdb=" CA ASP B 298 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.28e-02 6.10e+03 8.57e+00 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N THR G 6 " pdb=" CA THR G 6 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N THR A 9 " pdb=" CA THR A 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N SER R 86 " pdb=" CA SER R 86 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 8692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 11634 2.19 - 4.37: 136 4.37 - 6.56: 6 6.56 - 8.75: 0 8.75 - 10.93: 2 Bond angle restraints: 11778 Sorted by residual: angle pdb=" CB MET R 245 " pdb=" CG MET R 245 " pdb=" SD MET R 245 " ideal model delta sigma weight residual 112.70 123.63 -10.93 3.00e+00 1.11e-01 1.33e+01 angle pdb=" CA PRO R 355 " pdb=" N PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 112.00 107.61 4.39 1.40e+00 5.10e-01 9.82e+00 angle pdb=" C VAL R 234 " pdb=" CA VAL R 234 " pdb=" CB VAL R 234 " ideal model delta sigma weight residual 113.70 110.80 2.90 9.50e-01 1.11e+00 9.32e+00 angle pdb=" CB MET A 60 " pdb=" CG MET A 60 " pdb=" SD MET A 60 " ideal model delta sigma weight residual 112.70 121.61 -8.91 3.00e+00 1.11e-01 8.82e+00 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 122.08 126.34 -4.26 1.47e+00 4.63e-01 8.40e+00 ... (remaining 11773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4537 17.76 - 35.52: 514 35.52 - 53.28: 133 53.28 - 71.05: 21 71.05 - 88.81: 15 Dihedral angle restraints: 5220 sinusoidal: 2079 harmonic: 3141 Sorted by residual: dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 358 " pdb=" CB CYS R 358 " ideal model delta sinusoidal sigma weight residual -86.00 -166.20 80.20 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 28.26 64.74 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CA HIS B 311 " pdb=" C HIS B 311 " pdb=" N ASP B 312 " pdb=" CA ASP B 312 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 848 0.033 - 0.065: 344 0.065 - 0.098: 84 0.098 - 0.130: 45 0.130 - 0.163: 10 Chirality restraints: 1331 Sorted by residual: chirality pdb=" CA PRO R 285 " pdb=" N PRO R 285 " pdb=" C PRO R 285 " pdb=" CB PRO R 285 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA CYS R 358 " pdb=" N CYS R 358 " pdb=" C CYS R 358 " pdb=" CB CYS R 358 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CG LEU A 292 " pdb=" CB LEU A 292 " pdb=" CD1 LEU A 292 " pdb=" CD2 LEU A 292 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 1328 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 354 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO R 355 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO R 355 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO R 355 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 42 " -0.218 9.50e-02 1.11e+02 9.78e-02 6.34e+00 pdb=" NE ARG A 42 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 42 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 42 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 42 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 317 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO A 318 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 318 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 318 " 0.028 5.00e-02 4.00e+02 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 100 2.62 - 3.19: 7706 3.19 - 3.76: 12984 3.76 - 4.33: 18201 4.33 - 4.90: 30558 Nonbonded interactions: 69549 Sorted by model distance: nonbonded pdb=" OE2 GLU R 236 " pdb=" OH TYR R 269 " model vdw 2.050 3.040 nonbonded pdb=" OG SER B 147 " pdb=" OG SER B 160 " model vdw 2.050 3.040 nonbonded pdb=" O SER N 52 " pdb=" NH1 ARG N 72 " model vdw 2.170 3.120 nonbonded pdb=" OD1 ASP A 285 " pdb=" N LEU A 286 " model vdw 2.188 3.120 nonbonded pdb=" O ILE R 187 " pdb=" OG SER R 191 " model vdw 2.196 3.040 ... (remaining 69544 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 0.062 8697 Z= 0.245 Angle : 0.627 10.934 11778 Z= 0.361 Chirality : 0.042 0.163 1331 Planarity : 0.006 0.109 1498 Dihedral : 16.632 88.807 3174 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.65 % Allowed : 26.02 % Favored : 73.33 % 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: 0.79 (0.26), residues: 1062 helix: 1.53 (0.25), residues: 408 sheet: 0.34 (0.33), residues: 231 loop : -0.27 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 47 HIS 0.005 0.001 HIS A 347 PHE 0.021 0.002 PHE R 240 TYR 0.010 0.001 TYR N 95 ARG 0.012 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 277 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7158 (mtm110) cc_final: 0.6919 (mtm110) REVERT: A 252 ASP cc_start: 0.7628 (t0) cc_final: 0.7222 (t0) REVERT: A 279 LEU cc_start: 0.8810 (tp) cc_final: 0.8601 (mt) REVERT: A 357 VAL cc_start: 0.8666 (p) cc_final: 0.8406 (m) REVERT: B 204 CYS cc_start: 0.7895 (m) cc_final: 0.7629 (m) REVERT: B 217 MET cc_start: 0.6847 (ptt) cc_final: 0.6643 (ptp) REVERT: B 262 MET cc_start: 0.8301 (ttm) cc_final: 0.7929 (ttm) REVERT: R 365 LEU cc_start: 0.8549 (mt) cc_final: 0.8344 (mt) outliers start: 6 outliers final: 5 residues processed: 281 average time/residue: 1.1117 time to fit residues: 333.8837 Evaluate side-chains 262 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 257 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 378 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.0010 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 94 optimal weight: 0.6980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 261 ASN A 282 ASN B 119 ASN B 142 HIS B 237 ASN B 266 HIS R 104 ASN R 119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.148015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.126916 restraints weight = 12529.700| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.24 r_work: 0.3510 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8697 Z= 0.191 Angle : 0.588 7.231 11778 Z= 0.310 Chirality : 0.043 0.213 1331 Planarity : 0.005 0.070 1498 Dihedral : 5.124 37.938 1179 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.27 % Allowed : 21.51 % Favored : 73.23 % 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 (0.26), residues: 1062 helix: 1.77 (0.25), residues: 419 sheet: 0.43 (0.33), residues: 229 loop : -0.21 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 41 PHE 0.029 0.002 PHE R 278 TYR 0.015 0.001 TYR N 95 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7726 (mtm110) cc_final: 0.7306 (mtm110) REVERT: A 34 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7964 (ptmm) REVERT: A 252 ASP cc_start: 0.7875 (t0) cc_final: 0.7427 (t0) REVERT: A 256 LEU cc_start: 0.8463 (mt) cc_final: 0.8233 (mt) REVERT: A 317 GLU cc_start: 0.7324 (mp0) cc_final: 0.6115 (mp0) REVERT: A 320 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7197 (mt-10) REVERT: A 369 CYS cc_start: 0.8632 (m) cc_final: 0.8418 (m) REVERT: B 96 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7408 (ttp80) REVERT: B 173 THR cc_start: 0.8250 (m) cc_final: 0.7980 (t) REVERT: B 217 MET cc_start: 0.7169 (ptt) cc_final: 0.6917 (ptp) REVERT: B 262 MET cc_start: 0.8495 (ttm) cc_final: 0.8205 (ttm) REVERT: B 329 THR cc_start: 0.8645 (m) cc_final: 0.8221 (p) REVERT: B 333 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.6601 (t0) REVERT: N 21 SER cc_start: 0.8391 (t) cc_final: 0.8181 (p) REVERT: R 109 CYS cc_start: 0.7859 (m) cc_final: 0.7644 (p) REVERT: R 132 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6258 (ttm) outliers start: 49 outliers final: 24 residues processed: 279 average time/residue: 1.0839 time to fit residues: 323.6084 Evaluate side-chains 274 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 372 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 237 ASN B 259 GLN R 119 ASN R 373 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.143994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122822 restraints weight = 12717.395| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.23 r_work: 0.3462 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8697 Z= 0.375 Angle : 0.640 12.204 11778 Z= 0.335 Chirality : 0.046 0.234 1331 Planarity : 0.005 0.060 1498 Dihedral : 5.040 35.210 1174 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.05 % Allowed : 23.12 % Favored : 71.83 % 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: 0.85 (0.25), residues: 1062 helix: 1.65 (0.25), residues: 418 sheet: 0.34 (0.33), residues: 224 loop : -0.34 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.007 0.002 HIS A 347 PHE 0.028 0.002 PHE B 335 TYR 0.020 0.002 TYR N 60 ARG 0.007 0.001 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 258 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7132 (mtm110) REVERT: A 31 GLN cc_start: 0.7621 (tp-100) cc_final: 0.7251 (tp-100) REVERT: A 34 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7943 (ptmm) REVERT: A 252 ASP cc_start: 0.7926 (t0) cc_final: 0.7629 (t0) REVERT: A 255 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8111 (mmm-85) REVERT: A 317 GLU cc_start: 0.7368 (mp0) cc_final: 0.5832 (mp0) REVERT: A 320 GLU cc_start: 0.7733 (mt-10) cc_final: 0.6779 (mt-10) REVERT: A 336 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8283 (mm) REVERT: A 337 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7929 (mtm110) REVERT: A 369 CYS cc_start: 0.8601 (m) cc_final: 0.8390 (m) REVERT: B 19 ARG cc_start: 0.7929 (ttp-110) cc_final: 0.7678 (ttp80) REVERT: B 82 TRP cc_start: 0.8566 (m100) cc_final: 0.8083 (m100) REVERT: B 173 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8076 (t) REVERT: B 198 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8122 (mp) REVERT: B 212 ASP cc_start: 0.8217 (t0) cc_final: 0.7970 (t0) REVERT: B 262 MET cc_start: 0.8490 (ttm) cc_final: 0.8187 (ttm) REVERT: B 325 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7862 (ttm) REVERT: B 333 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7478 (t0) REVERT: N 21 SER cc_start: 0.8515 (t) cc_final: 0.8049 (p) REVERT: N 39 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: N 126 VAL cc_start: 0.7717 (t) cc_final: 0.7479 (m) REVERT: R 132 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6378 (ttm) REVERT: R 351 ASN cc_start: 0.7823 (t0) cc_final: 0.7009 (p0) outliers start: 47 outliers final: 25 residues processed: 273 average time/residue: 1.1313 time to fit residues: 329.6712 Evaluate side-chains 285 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 372 ILE Chi-restraints excluded: chain R residue 378 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 67 optimal weight: 0.0670 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 101 optimal weight: 0.0970 chunk 81 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 261 ASN B 119 ASN B 237 ASN R 119 ASN R 373 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.147531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126294 restraints weight = 12542.320| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.24 r_work: 0.3494 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8697 Z= 0.190 Angle : 0.582 12.236 11778 Z= 0.300 Chirality : 0.043 0.234 1331 Planarity : 0.005 0.054 1498 Dihedral : 4.705 38.226 1174 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 6.13 % Allowed : 23.44 % Favored : 70.43 % 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: 1.01 (0.26), residues: 1062 helix: 1.80 (0.25), residues: 421 sheet: 0.39 (0.33), residues: 224 loop : -0.26 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS B 311 PHE 0.015 0.002 PHE N 29 TYR 0.021 0.001 TYR N 60 ARG 0.007 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 254 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7675 (mtm110) cc_final: 0.7041 (mtm110) REVERT: A 31 GLN cc_start: 0.7489 (tp-100) cc_final: 0.7065 (tp40) REVERT: A 34 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7895 (ptmm) REVERT: A 252 ASP cc_start: 0.7926 (t0) cc_final: 0.7643 (t0) REVERT: A 255 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.8044 (mmm-85) REVERT: A 317 GLU cc_start: 0.7369 (mp0) cc_final: 0.5751 (mp0) REVERT: A 320 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6657 (mt-10) REVERT: A 337 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7893 (mtm110) REVERT: B 19 ARG cc_start: 0.7840 (ttp-110) cc_final: 0.7480 (ttp80) REVERT: B 173 THR cc_start: 0.8368 (m) cc_final: 0.8118 (t) REVERT: B 212 ASP cc_start: 0.8159 (t0) cc_final: 0.7896 (t0) REVERT: B 220 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7811 (mm-40) REVERT: B 243 THR cc_start: 0.8498 (t) cc_final: 0.8238 (p) REVERT: B 262 MET cc_start: 0.8480 (ttm) cc_final: 0.8191 (ttm) REVERT: B 283 ARG cc_start: 0.8626 (tpt-90) cc_final: 0.8273 (tpp80) REVERT: B 325 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7775 (ttm) REVERT: B 333 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7417 (t0) REVERT: N 21 SER cc_start: 0.8512 (t) cc_final: 0.8046 (p) REVERT: N 39 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: R 132 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6170 (ttm) REVERT: R 173 MET cc_start: 0.7901 (tpp) cc_final: 0.7492 (mpp) outliers start: 57 outliers final: 29 residues processed: 277 average time/residue: 1.1402 time to fit residues: 337.3921 Evaluate side-chains 281 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 372 ILE Chi-restraints excluded: chain R residue 378 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 96 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 237 ASN R 104 ASN R 119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.147458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126407 restraints weight = 12559.763| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.26 r_work: 0.3501 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8697 Z= 0.180 Angle : 0.574 12.608 11778 Z= 0.295 Chirality : 0.043 0.226 1331 Planarity : 0.004 0.052 1498 Dihedral : 4.522 35.352 1174 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.59 % Allowed : 25.27 % Favored : 69.14 % 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: 1.08 (0.26), residues: 1062 helix: 1.89 (0.25), residues: 417 sheet: 0.41 (0.33), residues: 224 loop : -0.23 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 PHE 0.026 0.002 PHE R 278 TYR 0.018 0.001 TYR N 60 ARG 0.009 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 250 time to evaluate : 1.020 Fit side-chains REVERT: A 20 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7028 (mtm110) REVERT: A 31 GLN cc_start: 0.7549 (tp-100) cc_final: 0.7141 (tp40) REVERT: A 34 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7892 (ptmm) REVERT: A 252 ASP cc_start: 0.7941 (t0) cc_final: 0.7643 (t0) REVERT: A 255 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.8048 (mmm-85) REVERT: A 264 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8511 (ttmm) REVERT: A 317 GLU cc_start: 0.7344 (mp0) cc_final: 0.5687 (mp0) REVERT: A 320 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6599 (mt-10) REVERT: B 19 ARG cc_start: 0.7855 (ttp-110) cc_final: 0.7479 (ttp80) REVERT: B 173 THR cc_start: 0.8390 (m) cc_final: 0.8149 (t) REVERT: B 212 ASP cc_start: 0.8121 (t0) cc_final: 0.7826 (t0) REVERT: B 217 MET cc_start: 0.7480 (ptp) cc_final: 0.7205 (pmm) REVERT: B 243 THR cc_start: 0.8469 (t) cc_final: 0.8178 (p) REVERT: B 262 MET cc_start: 0.8481 (ttm) cc_final: 0.8181 (ttm) REVERT: B 316 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8134 (p) REVERT: B 333 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.6611 (t0) REVERT: B 335 PHE cc_start: 0.7505 (m-80) cc_final: 0.7269 (m-80) REVERT: B 337 LYS cc_start: 0.8859 (mttt) cc_final: 0.8656 (mttt) REVERT: N 21 SER cc_start: 0.8609 (t) cc_final: 0.8150 (p) REVERT: P 13 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.8076 (t80) REVERT: R 132 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.6307 (ttm) REVERT: R 173 MET cc_start: 0.7854 (mpp) cc_final: 0.7437 (mpp) REVERT: R 222 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7898 (mp) REVERT: R 240 PHE cc_start: 0.8457 (m-80) cc_final: 0.7890 (m-10) REVERT: R 277 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7685 (mt) outliers start: 52 outliers final: 30 residues processed: 269 average time/residue: 1.1380 time to fit residues: 326.6646 Evaluate side-chains 285 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 247 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain P residue 13 TYR Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 0.0000 chunk 94 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 261 ASN B 125 ASN B 237 ASN R 373 ASN R 378 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.145870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125226 restraints weight = 12507.519| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.22 r_work: 0.3494 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8697 Z= 0.225 Angle : 0.584 12.024 11778 Z= 0.300 Chirality : 0.043 0.198 1331 Planarity : 0.004 0.049 1498 Dihedral : 4.537 33.940 1174 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.05 % Allowed : 25.91 % Favored : 69.03 % 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: 1.08 (0.25), residues: 1062 helix: 1.93 (0.25), residues: 415 sheet: 0.39 (0.33), residues: 222 loop : -0.26 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 PHE 0.016 0.002 PHE N 108 TYR 0.024 0.001 TYR N 60 ARG 0.007 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 259 time to evaluate : 0.904 Fit side-chains REVERT: A 20 ARG cc_start: 0.7635 (mtm110) cc_final: 0.7024 (mtm110) REVERT: A 31 GLN cc_start: 0.7543 (tp-100) cc_final: 0.7166 (tp40) REVERT: A 34 LYS cc_start: 0.8267 (ptmm) cc_final: 0.7907 (ptmm) REVERT: A 252 ASP cc_start: 0.7932 (t0) cc_final: 0.7648 (t0) REVERT: A 255 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.8077 (mmm-85) REVERT: A 317 GLU cc_start: 0.7388 (mp0) cc_final: 0.5746 (mp0) REVERT: A 320 GLU cc_start: 0.7797 (mt-10) cc_final: 0.6607 (mt-10) REVERT: A 337 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7926 (mtm110) REVERT: B 19 ARG cc_start: 0.7868 (ttp-110) cc_final: 0.7512 (ttp80) REVERT: B 173 THR cc_start: 0.8410 (m) cc_final: 0.8156 (t) REVERT: B 212 ASP cc_start: 0.8181 (t0) cc_final: 0.7863 (t0) REVERT: B 217 MET cc_start: 0.7454 (ptp) cc_final: 0.7254 (pmm) REVERT: B 243 THR cc_start: 0.8473 (t) cc_final: 0.8184 (p) REVERT: B 262 MET cc_start: 0.8475 (ttm) cc_final: 0.8176 (ttm) REVERT: B 283 ARG cc_start: 0.8663 (tpt-90) cc_final: 0.8195 (tpp80) REVERT: B 316 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.8149 (p) REVERT: B 333 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.6539 (t0) REVERT: B 335 PHE cc_start: 0.7531 (m-80) cc_final: 0.7235 (m-80) REVERT: N 21 SER cc_start: 0.8580 (t) cc_final: 0.8169 (p) REVERT: N 39 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: P 13 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.8032 (t80) REVERT: R 132 MET cc_start: 0.6454 (OUTLIER) cc_final: 0.6225 (ttm) REVERT: R 173 MET cc_start: 0.7817 (mpp) cc_final: 0.7383 (mpp) REVERT: R 222 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7908 (mp) REVERT: R 240 PHE cc_start: 0.8429 (m-80) cc_final: 0.7862 (m-10) outliers start: 47 outliers final: 29 residues processed: 281 average time/residue: 1.1229 time to fit residues: 337.3706 Evaluate side-chains 286 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain P residue 13 TYR Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 378 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 0.0770 chunk 79 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 91 optimal weight: 0.3980 chunk 78 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 119 ASN B 237 ASN B 266 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.146553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125784 restraints weight = 12594.037| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.24 r_work: 0.3505 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8697 Z= 0.189 Angle : 0.591 10.436 11778 Z= 0.301 Chirality : 0.044 0.326 1331 Planarity : 0.004 0.048 1498 Dihedral : 4.453 34.037 1174 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.05 % Allowed : 26.13 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1062 helix: 1.98 (0.25), residues: 415 sheet: 0.40 (0.34), residues: 222 loop : -0.24 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 PHE 0.013 0.002 PHE N 108 TYR 0.022 0.001 TYR N 60 ARG 0.006 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 254 time to evaluate : 0.735 Fit side-chains REVERT: A 20 ARG cc_start: 0.7629 (mtm110) cc_final: 0.7009 (mtm110) REVERT: A 31 GLN cc_start: 0.7525 (tp-100) cc_final: 0.7158 (tp40) REVERT: A 34 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7901 (ptmm) REVERT: A 56 ILE cc_start: 0.5227 (OUTLIER) cc_final: 0.4691 (tt) REVERT: A 214 VAL cc_start: 0.8664 (t) cc_final: 0.8445 (t) REVERT: A 252 ASP cc_start: 0.7922 (t0) cc_final: 0.7622 (t0) REVERT: A 255 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.8039 (mmm-85) REVERT: A 264 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8517 (ttmm) REVERT: A 317 GLU cc_start: 0.7388 (mp0) cc_final: 0.5670 (mp0) REVERT: A 320 GLU cc_start: 0.7773 (mt-10) cc_final: 0.6539 (mt-10) REVERT: B 19 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.7521 (ttp80) REVERT: B 173 THR cc_start: 0.8418 (m) cc_final: 0.8169 (t) REVERT: B 198 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8281 (mp) REVERT: B 212 ASP cc_start: 0.8166 (t0) cc_final: 0.7842 (t0) REVERT: B 217 MET cc_start: 0.7435 (ptp) cc_final: 0.7176 (pmm) REVERT: B 243 THR cc_start: 0.8469 (t) cc_final: 0.8175 (p) REVERT: B 262 MET cc_start: 0.8478 (ttm) cc_final: 0.8187 (ttm) REVERT: B 283 ARG cc_start: 0.8667 (tpt-90) cc_final: 0.8215 (tpp80) REVERT: B 333 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.6526 (t0) REVERT: N 21 SER cc_start: 0.8601 (t) cc_final: 0.8172 (p) REVERT: N 39 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: P 13 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.8080 (t80) REVERT: R 104 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.7950 (m110) REVERT: R 132 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.6180 (ttm) REVERT: R 173 MET cc_start: 0.7836 (mpp) cc_final: 0.7390 (mpp) REVERT: R 240 PHE cc_start: 0.8396 (m-80) cc_final: 0.7863 (m-10) REVERT: R 317 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7665 (mm-40) outliers start: 47 outliers final: 29 residues processed: 271 average time/residue: 1.1068 time to fit residues: 320.3376 Evaluate side-chains 276 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 238 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 13 TYR Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 374 MET Chi-restraints excluded: chain R residue 378 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 261 ASN B 119 ASN B 237 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.142969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122096 restraints weight = 12731.735| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.23 r_work: 0.3452 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 8697 Z= 0.436 Angle : 0.689 10.043 11778 Z= 0.359 Chirality : 0.049 0.301 1331 Planarity : 0.005 0.046 1498 Dihedral : 4.933 37.387 1174 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.27 % Allowed : 27.20 % Favored : 67.53 % 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: 0.81 (0.25), residues: 1062 helix: 1.68 (0.25), residues: 420 sheet: 0.17 (0.33), residues: 222 loop : -0.35 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.009 0.002 HIS B 311 PHE 0.032 0.003 PHE B 335 TYR 0.021 0.002 TYR N 60 ARG 0.013 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 254 time to evaluate : 1.052 Fit side-chains REVERT: A 20 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7169 (mtm110) REVERT: A 31 GLN cc_start: 0.7560 (tp-100) cc_final: 0.7307 (tp40) REVERT: A 214 VAL cc_start: 0.8814 (t) cc_final: 0.8587 (t) REVERT: A 252 ASP cc_start: 0.7952 (t0) cc_final: 0.7671 (t0) REVERT: A 255 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.8109 (mmm-85) REVERT: A 317 GLU cc_start: 0.7371 (mp0) cc_final: 0.5574 (mp0) REVERT: A 320 GLU cc_start: 0.7751 (mt-10) cc_final: 0.6434 (mt-10) REVERT: A 332 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8034 (ttt90) REVERT: A 336 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8237 (mm) REVERT: A 346 ARG cc_start: 0.8395 (mmm160) cc_final: 0.8168 (mmm160) REVERT: B 19 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7434 (ttp-110) REVERT: B 173 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8187 (t) REVERT: B 198 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8313 (mp) REVERT: B 212 ASP cc_start: 0.8230 (t0) cc_final: 0.7884 (t0) REVERT: B 217 MET cc_start: 0.7376 (ptp) cc_final: 0.7135 (pmm) REVERT: B 243 THR cc_start: 0.8550 (t) cc_final: 0.8299 (p) REVERT: B 262 MET cc_start: 0.8475 (ttm) cc_final: 0.8179 (ttm) REVERT: B 333 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7558 (t0) REVERT: N 21 SER cc_start: 0.8551 (t) cc_final: 0.8138 (p) REVERT: N 39 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: R 132 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6203 (ttm) REVERT: R 173 MET cc_start: 0.7891 (mpp) cc_final: 0.7380 (mpp) REVERT: R 222 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7886 (mp) REVERT: R 327 CYS cc_start: 0.8346 (m) cc_final: 0.8078 (m) outliers start: 49 outliers final: 34 residues processed: 279 average time/residue: 1.1121 time to fit residues: 331.3840 Evaluate side-chains 288 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 372 ILE Chi-restraints excluded: chain R residue 378 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 4 optimal weight: 0.0170 chunk 76 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 96 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 227 GLN A 261 ASN B 119 ASN B 293 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN R 378 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.125390 restraints weight = 12770.265| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.24 r_work: 0.3501 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8697 Z= 0.196 Angle : 0.640 11.582 11778 Z= 0.326 Chirality : 0.045 0.259 1331 Planarity : 0.005 0.048 1498 Dihedral : 4.585 35.180 1174 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.73 % Allowed : 28.82 % Favored : 66.45 % 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: 0.85 (0.25), residues: 1062 helix: 1.73 (0.25), residues: 422 sheet: 0.21 (0.33), residues: 222 loop : -0.37 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.027 0.002 PHE N 29 TYR 0.025 0.001 TYR N 60 ARG 0.015 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 0.954 Fit side-chains REVERT: A 20 ARG cc_start: 0.7609 (mtm110) cc_final: 0.7013 (mtm110) REVERT: A 31 GLN cc_start: 0.7530 (tp-100) cc_final: 0.7169 (tp40) REVERT: A 34 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7917 (ptmm) REVERT: A 252 ASP cc_start: 0.7956 (t0) cc_final: 0.7581 (t0) REVERT: A 255 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: A 317 GLU cc_start: 0.7394 (mp0) cc_final: 0.5618 (mp0) REVERT: A 320 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6463 (mt-10) REVERT: A 346 ARG cc_start: 0.8418 (mmm160) cc_final: 0.8177 (mmm160) REVERT: A 368 ASP cc_start: 0.7213 (m-30) cc_final: 0.6980 (m-30) REVERT: B 19 ARG cc_start: 0.7860 (ttp-110) cc_final: 0.7486 (ttp80) REVERT: B 173 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8223 (t) REVERT: B 198 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8309 (mp) REVERT: B 212 ASP cc_start: 0.8186 (t0) cc_final: 0.7843 (t0) REVERT: B 217 MET cc_start: 0.7412 (ptp) cc_final: 0.7186 (pmm) REVERT: B 243 THR cc_start: 0.8470 (t) cc_final: 0.8166 (p) REVERT: B 262 MET cc_start: 0.8463 (ttm) cc_final: 0.8187 (ttm) REVERT: B 283 ARG cc_start: 0.8663 (tpt-90) cc_final: 0.8416 (tpp80) REVERT: B 298 ASP cc_start: 0.7831 (t70) cc_final: 0.7512 (p0) REVERT: B 300 LEU cc_start: 0.8324 (mp) cc_final: 0.8106 (mm) REVERT: B 316 SER cc_start: 0.8419 (OUTLIER) cc_final: 0.8113 (p) REVERT: B 333 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7412 (t0) REVERT: N 21 SER cc_start: 0.8621 (t) cc_final: 0.8233 (p) REVERT: N 39 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: P 13 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.8070 (t80) REVERT: R 132 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.6142 (ttm) REVERT: R 173 MET cc_start: 0.7871 (mpp) cc_final: 0.7384 (mpp) REVERT: R 222 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7904 (mp) REVERT: R 240 PHE cc_start: 0.8384 (m-80) cc_final: 0.7824 (m-10) REVERT: R 266 MET cc_start: 0.6439 (mmp) cc_final: 0.6040 (mmp) REVERT: R 368 ASP cc_start: 0.7919 (m-30) cc_final: 0.7675 (m-30) outliers start: 44 outliers final: 30 residues processed: 266 average time/residue: 1.1507 time to fit residues: 326.3088 Evaluate side-chains 285 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 13 TYR Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 227 GLN A 261 ASN B 119 ASN B 237 ASN B 266 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124967 restraints weight = 12585.753| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.21 r_work: 0.3485 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8697 Z= 0.265 Angle : 0.648 11.368 11778 Z= 0.333 Chirality : 0.046 0.294 1331 Planarity : 0.005 0.053 1498 Dihedral : 4.641 35.037 1174 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.30 % Allowed : 29.46 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1062 helix: 1.73 (0.26), residues: 421 sheet: 0.17 (0.33), residues: 222 loop : -0.37 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 PHE 0.037 0.002 PHE R 278 TYR 0.024 0.002 TYR N 60 ARG 0.014 0.001 ARG A 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 242 time to evaluate : 0.986 Fit side-chains REVERT: A 20 ARG cc_start: 0.7652 (mtm110) cc_final: 0.7124 (mtm110) REVERT: A 31 GLN cc_start: 0.7556 (tp-100) cc_final: 0.7209 (tp40) REVERT: A 34 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7946 (ptmm) REVERT: A 60 MET cc_start: 0.6031 (mpt) cc_final: 0.5273 (mpt) REVERT: A 252 ASP cc_start: 0.7941 (t0) cc_final: 0.7568 (t0) REVERT: A 255 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8063 (mmm-85) REVERT: A 317 GLU cc_start: 0.7382 (mp0) cc_final: 0.5593 (mp0) REVERT: A 320 GLU cc_start: 0.7786 (mt-10) cc_final: 0.6498 (mt-10) REVERT: A 346 ARG cc_start: 0.8412 (mmm160) cc_final: 0.8172 (mmm160) REVERT: A 368 ASP cc_start: 0.7241 (m-30) cc_final: 0.7016 (m-30) REVERT: B 19 ARG cc_start: 0.7870 (ttp-110) cc_final: 0.7490 (ttp80) REVERT: B 49 ARG cc_start: 0.8667 (mtp85) cc_final: 0.8328 (mmm-85) REVERT: B 173 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8176 (t) REVERT: B 212 ASP cc_start: 0.8200 (t0) cc_final: 0.7858 (t0) REVERT: B 217 MET cc_start: 0.7413 (ptp) cc_final: 0.7179 (pmm) REVERT: B 243 THR cc_start: 0.8485 (t) cc_final: 0.8193 (p) REVERT: B 262 MET cc_start: 0.8480 (ttm) cc_final: 0.8185 (ttm) REVERT: B 283 ARG cc_start: 0.8675 (tpt-90) cc_final: 0.8387 (tpp80) REVERT: B 298 ASP cc_start: 0.7914 (t70) cc_final: 0.7581 (p0) REVERT: B 300 LEU cc_start: 0.8343 (mp) cc_final: 0.8132 (mm) REVERT: B 316 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8163 (p) REVERT: B 333 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7382 (t0) REVERT: N 21 SER cc_start: 0.8614 (t) cc_final: 0.8220 (p) REVERT: N 39 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: P 13 TYR cc_start: 0.8356 (t80) cc_final: 0.8015 (t80) REVERT: R 132 MET cc_start: 0.6417 (OUTLIER) cc_final: 0.6166 (ttm) REVERT: R 173 MET cc_start: 0.7871 (mpp) cc_final: 0.7368 (mpp) REVERT: R 222 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7903 (mp) REVERT: R 240 PHE cc_start: 0.8381 (m-80) cc_final: 0.7813 (m-10) REVERT: R 248 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7810 (mtpt) REVERT: R 266 MET cc_start: 0.6529 (mmp) cc_final: 0.6174 (mmp) outliers start: 40 outliers final: 28 residues processed: 264 average time/residue: 1.1283 time to fit residues: 318.2377 Evaluate side-chains 275 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain R residue 379 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 60 optimal weight: 0.0870 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 227 GLN A 261 ASN B 119 ASN B 293 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.146493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.125854 restraints weight = 12811.559| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.26 r_work: 0.3501 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8697 Z= 0.198 Angle : 0.636 10.734 11778 Z= 0.324 Chirality : 0.045 0.283 1331 Planarity : 0.005 0.050 1498 Dihedral : 4.528 33.765 1174 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.41 % Allowed : 29.14 % Favored : 66.45 % 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: 0.80 (0.25), residues: 1062 helix: 1.70 (0.25), residues: 423 sheet: 0.12 (0.33), residues: 219 loop : -0.38 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS B 311 PHE 0.026 0.002 PHE N 29 TYR 0.024 0.001 TYR N 60 ARG 0.014 0.001 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7408.95 seconds wall clock time: 131 minutes 14.47 seconds (7874.47 seconds total)