Starting phenix.real_space_refine on Wed Sep 17 11:53:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xve_38702/09_2025/8xve_38702.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xve_38702/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xve_38702/09_2025/8xve_38702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xve_38702/09_2025/8xve_38702.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xve_38702/09_2025/8xve_38702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xve_38702/09_2025/8xve_38702.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.97, per 1000 atoms: 0.23 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: 0.50 Conformation dependent library (CDL) restraints added in 369.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.21 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: 1.20 Time building geometry restraints manager: 0.75 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.350 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.800 ------------------------------------------------------------------------------- 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 8701 Z= 0.188 Angle : 0.628 10.934 11786 Z= 0.362 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 : 7.93 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (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 ARG 0.012 0.001 ARG A 42 TYR 0.010 0.001 TYR N 95 PHE 0.021 0.002 PHE R 240 TRP 0.014 0.002 TRP N 47 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8697) covalent geometry : angle 0.62659 (11778) SS BOND : bond 0.00727 ( 4) SS BOND : angle 1.85191 ( 8) hydrogen bonds : bond 0.17200 ( 454) hydrogen bonds : angle 6.55326 ( 1296) *********************** 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 : 0.296 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: 0.7246 (t0) REVERT: A 255 ARG cc_start: 0.8154 (mmm-85) cc_final: 0.7718 (mmm-85) 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: 0.8405 (m) REVERT: B 204 CYS cc_start: 0.7895 (m) cc_final: 0.7630 (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: 0.5294 time to fit residues: 158.4667 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 : 0.350 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 261 ASN A 282 ASN B 119 ASN B 237 ASN B 266 HIS R 104 ASN R 119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125367 restraints weight = 12609.241| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.26 r_work: 0.3486 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8701 Z= 0.169 Angle : 0.611 7.655 11786 Z= 0.322 Chirality : 0.044 0.233 1331 Planarity : 0.005 0.071 1498 Dihedral : 5.244 38.327 1179 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 5.27 % Allowed : 21.83 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.26), residues: 1062 helix: 1.65 (0.25), residues: 419 sheet: 0.36 (0.33), residues: 231 loop : -0.21 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 27 TYR 0.016 0.002 TYR N 95 PHE 0.030 0.002 PHE R 278 TRP 0.015 0.002 TRP B 339 HIS 0.006 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8697) covalent geometry : angle 0.60819 (11778) SS BOND : bond 0.00409 ( 4) SS BOND : angle 2.49408 ( 8) hydrogen bonds : bond 0.05135 ( 454) hydrogen bonds : angle 4.92460 ( 1296) *********************** 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 308 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7758 (mtm110) cc_final: 0.7352 (mtm110) REVERT: A 34 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7943 (ptmm) REVERT: A 252 ASP cc_start: 0.7871 (t0) cc_final: 0.7433 (t0) REVERT: A 317 GLU cc_start: 0.7318 (mp0) cc_final: 0.6160 (mp0) REVERT: A 320 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7181 (mt-10) REVERT: A 369 CYS cc_start: 0.8623 (m) cc_final: 0.8422 (m) REVERT: B 96 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7417 (ttp80) REVERT: B 173 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.8007 (t) REVERT: B 212 ASP cc_start: 0.8130 (t0) cc_final: 0.7927 (t0) REVERT: B 217 MET cc_start: 0.7115 (ptt) cc_final: 0.6864 (ptp) REVERT: B 262 MET cc_start: 0.8493 (ttm) cc_final: 0.8190 (ttm) REVERT: B 329 THR cc_start: 0.8646 (m) cc_final: 0.8221 (p) REVERT: B 333 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.6711 (t0) REVERT: N 21 SER cc_start: 0.8431 (t) cc_final: 0.8183 (p) REVERT: N 30 SER cc_start: 0.8805 (m) cc_final: 0.8549 (p) REVERT: R 109 CYS cc_start: 0.7798 (m) cc_final: 0.7499 (p) REVERT: R 132 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6272 (ttm) outliers start: 49 outliers final: 24 residues processed: 274 average time/residue: 0.5229 time to fit residues: 152.9721 Evaluate side-chains 274 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS 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 173 THR 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 G residue 46 LYS 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 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 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 6 optimal weight: 0.0970 chunk 94 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 0.0270 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 R 119 ASN ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127229 restraints weight = 12502.430| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.24 r_work: 0.3515 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8701 Z= 0.124 Angle : 0.572 12.389 11786 Z= 0.295 Chirality : 0.043 0.225 1331 Planarity : 0.004 0.061 1498 Dihedral : 4.713 41.431 1174 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.27 % Allowed : 22.26 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.26), residues: 1062 helix: 1.85 (0.25), residues: 421 sheet: 0.47 (0.34), residues: 222 loop : -0.24 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.021 0.001 TYR N 60 PHE 0.017 0.002 PHE R 240 TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8697) covalent geometry : angle 0.56991 (11778) SS BOND : bond 0.00334 ( 4) SS BOND : angle 1.90786 ( 8) hydrogen bonds : bond 0.04337 ( 454) hydrogen bonds : angle 4.59528 ( 1296) *********************** 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 304 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 0.339 Fit side-chains REVERT: A 20 ARG cc_start: 0.7661 (mtm110) cc_final: 0.7216 (mtm110) REVERT: A 31 GLN cc_start: 0.7467 (tp-100) cc_final: 0.7107 (tp-100) REVERT: A 34 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7903 (ptmm) REVERT: A 252 ASP cc_start: 0.7914 (t0) cc_final: 0.7537 (t0) REVERT: A 317 GLU cc_start: 0.7345 (mp0) cc_final: 0.5769 (mp0) REVERT: A 320 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7003 (mt-10) REVERT: A 337 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7802 (mtm110) REVERT: A 369 CYS cc_start: 0.8636 (m) cc_final: 0.8425 (m) REVERT: B 134 ARG cc_start: 0.8336 (ttm110) cc_final: 0.8041 (ttp-110) REVERT: B 173 THR cc_start: 0.8362 (m) cc_final: 0.8131 (t) REVERT: B 217 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6887 (ptp) REVERT: B 262 MET cc_start: 0.8477 (ttm) cc_final: 0.8172 (ttm) REVERT: B 325 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7851 (ttp) REVERT: B 333 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7356 (t0) REVERT: N 21 SER cc_start: 0.8394 (t) cc_final: 0.8163 (p) REVERT: R 132 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6343 (ttm) REVERT: R 173 MET cc_start: 0.7916 (tpp) cc_final: 0.7545 (mpp) REVERT: R 288 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8230 (tt) outliers start: 49 outliers final: 24 residues processed: 274 average time/residue: 0.5362 time to fit residues: 156.7371 Evaluate side-chains 283 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 313 ASP 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 122 SER Chi-restraints excluded: chain B residue 217 MET 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 N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER 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 256 LEU Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 341 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 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 36 optimal weight: 0.0670 chunk 30 optimal weight: 1.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 125 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 259 GLN R 119 ASN ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.146484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125688 restraints weight = 12848.425| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.27 r_work: 0.3502 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8701 Z= 0.137 Angle : 0.572 13.197 11786 Z= 0.294 Chirality : 0.043 0.228 1331 Planarity : 0.004 0.054 1498 Dihedral : 4.572 39.378 1174 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.27 % Allowed : 24.41 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.26), residues: 1062 helix: 2.03 (0.25), residues: 414 sheet: 0.45 (0.33), residues: 224 loop : -0.21 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 19 TYR 0.019 0.001 TYR N 60 PHE 0.015 0.002 PHE N 108 TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8697) covalent geometry : angle 0.57053 (11778) SS BOND : bond 0.00455 ( 4) SS BOND : angle 1.41183 ( 8) hydrogen bonds : bond 0.04213 ( 454) hydrogen bonds : angle 4.55600 ( 1296) *********************** 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 308 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 0.312 Fit side-chains REVERT: A 20 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7012 (mtm110) REVERT: A 31 GLN cc_start: 0.7501 (tp-100) cc_final: 0.7127 (tp40) REVERT: A 34 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7921 (ptmm) REVERT: A 252 ASP cc_start: 0.7952 (t0) cc_final: 0.7571 (t0) REVERT: A 317 GLU cc_start: 0.7354 (mp0) cc_final: 0.5772 (mp0) REVERT: A 320 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6724 (mt-10) REVERT: A 369 CYS cc_start: 0.8654 (m) cc_final: 0.8453 (m) REVERT: B 173 THR cc_start: 0.8386 (m) cc_final: 0.8154 (t) REVERT: B 198 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8125 (mp) REVERT: B 212 ASP cc_start: 0.8155 (t0) cc_final: 0.7946 (t0) REVERT: B 243 THR cc_start: 0.8492 (t) cc_final: 0.8224 (p) REVERT: B 262 MET cc_start: 0.8495 (ttm) cc_final: 0.8195 (ttm) REVERT: B 283 ARG cc_start: 0.8564 (tpt-90) cc_final: 0.8151 (tpp80) REVERT: B 325 MET cc_start: 0.7997 (ttm) cc_final: 0.7744 (ttm) REVERT: B 333 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.6673 (t0) REVERT: B 335 PHE cc_start: 0.7493 (m-80) cc_final: 0.7266 (m-80) REVERT: N 21 SER cc_start: 0.8502 (t) cc_final: 0.8021 (p) REVERT: P 13 TYR cc_start: 0.8424 (t80) cc_final: 0.8046 (t80) REVERT: R 132 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6187 (ttm) REVERT: R 173 MET cc_start: 0.7907 (tpp) cc_final: 0.7530 (mpp) REVERT: R 361 LEU cc_start: 0.7570 (tp) cc_final: 0.7202 (tm) outliers start: 49 outliers final: 25 residues processed: 273 average time/residue: 0.5179 time to fit residues: 150.7911 Evaluate side-chains 272 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 242 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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 90 VAL 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 317 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 35 ASN 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 P residue 17 LEU 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 176 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 300 MET Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 372 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 78 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 237 ASN ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN R 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.144942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124024 restraints weight = 12663.010| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.24 r_work: 0.3486 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8701 Z= 0.181 Angle : 0.587 11.480 11786 Z= 0.304 Chirality : 0.044 0.244 1331 Planarity : 0.004 0.050 1498 Dihedral : 4.614 34.673 1174 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.70 % Allowed : 25.05 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.25), residues: 1062 helix: 1.88 (0.25), residues: 420 sheet: 0.37 (0.33), residues: 224 loop : -0.27 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 219 TYR 0.020 0.001 TYR N 60 PHE 0.019 0.002 PHE N 108 TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8697) covalent geometry : angle 0.58558 (11778) SS BOND : bond 0.00462 ( 4) SS BOND : angle 1.39310 ( 8) hydrogen bonds : bond 0.04408 ( 454) hydrogen bonds : angle 4.61955 ( 1296) *********************** 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 307 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 254 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7670 (mtm110) cc_final: 0.7070 (mtm110) REVERT: A 31 GLN cc_start: 0.7619 (tp-100) cc_final: 0.7205 (tp40) REVERT: A 34 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7892 (ptmm) REVERT: A 252 ASP cc_start: 0.7955 (t0) cc_final: 0.7607 (t0) REVERT: A 317 GLU cc_start: 0.7368 (mp0) cc_final: 0.5718 (mp0) REVERT: A 320 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6605 (mt-10) REVERT: A 337 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7944 (mtm110) REVERT: B 19 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7655 (ttp80) REVERT: B 173 THR cc_start: 0.8387 (m) cc_final: 0.8142 (t) REVERT: B 197 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.7827 (mmm-85) REVERT: B 212 ASP cc_start: 0.8154 (t0) cc_final: 0.7915 (t0) REVERT: B 243 THR cc_start: 0.8502 (t) cc_final: 0.8224 (p) REVERT: B 262 MET cc_start: 0.8478 (ttm) cc_final: 0.8182 (ttm) REVERT: B 298 ASP cc_start: 0.7924 (t70) cc_final: 0.7423 (p0) REVERT: B 325 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7773 (ttm) REVERT: B 333 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.6614 (t0) REVERT: B 335 PHE cc_start: 0.7642 (m-80) cc_final: 0.7252 (m-80) REVERT: N 21 SER cc_start: 0.8499 (t) cc_final: 0.8061 (p) REVERT: N 39 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: R 132 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6101 (ttm) REVERT: R 155 ILE cc_start: 0.8443 (mm) cc_final: 0.8241 (tp) REVERT: R 173 MET cc_start: 0.7897 (tpp) cc_final: 0.7500 (mpp) REVERT: R 365 LEU cc_start: 0.8428 (mt) cc_final: 0.8207 (mt) outliers start: 53 outliers final: 30 residues processed: 274 average time/residue: 0.4876 time to fit residues: 143.0618 Evaluate side-chains 294 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 90 VAL Chi-restraints excluded: chain B residue 187 VAL 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 316 SER 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 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 176 LEU Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 300 MET Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 372 ILE Chi-restraints excluded: chain R residue 378 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124791 restraints weight = 12568.674| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.23 r_work: 0.3490 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8701 Z= 0.167 Angle : 0.594 8.047 11786 Z= 0.307 Chirality : 0.044 0.269 1331 Planarity : 0.005 0.048 1498 Dihedral : 4.573 34.548 1174 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.81 % Allowed : 25.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.25), residues: 1062 helix: 1.94 (0.25), residues: 415 sheet: 0.39 (0.33), residues: 222 loop : -0.28 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 219 TYR 0.021 0.001 TYR N 60 PHE 0.017 0.002 PHE N 108 TRP 0.014 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8697) covalent geometry : angle 0.59375 (11778) SS BOND : bond 0.00377 ( 4) SS BOND : angle 1.26120 ( 8) hydrogen bonds : bond 0.04286 ( 454) hydrogen bonds : angle 4.58956 ( 1296) *********************** 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 308 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 254 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7652 (mtm110) cc_final: 0.7056 (mtm110) REVERT: A 31 GLN cc_start: 0.7581 (tp-100) cc_final: 0.7202 (tp40) REVERT: A 34 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7902 (ptmm) REVERT: A 249 ASP cc_start: 0.8038 (t0) cc_final: 0.7769 (t0) REVERT: A 252 ASP cc_start: 0.7943 (t0) cc_final: 0.7566 (t0) REVERT: A 255 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.7947 (mmm-85) REVERT: A 283 LYS cc_start: 0.8677 (mttt) cc_final: 0.8460 (mttt) REVERT: A 317 GLU cc_start: 0.7395 (mp0) cc_final: 0.5690 (mp0) REVERT: A 320 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6551 (mt-10) REVERT: A 337 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7941 (mtm110) REVERT: B 19 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7615 (ttp80) REVERT: B 96 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7531 (ttp80) REVERT: B 173 THR cc_start: 0.8407 (m) cc_final: 0.8160 (t) REVERT: B 198 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8342 (mp) REVERT: B 212 ASP cc_start: 0.8155 (t0) cc_final: 0.7868 (t0) REVERT: B 243 THR cc_start: 0.8485 (t) cc_final: 0.8209 (p) REVERT: B 262 MET cc_start: 0.8459 (ttm) cc_final: 0.8168 (ttm) REVERT: B 325 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7754 (ttp) REVERT: B 333 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.6580 (t0) REVERT: B 335 PHE cc_start: 0.7604 (m-80) cc_final: 0.7270 (m-80) REVERT: N 21 SER cc_start: 0.8562 (t) cc_final: 0.8187 (p) REVERT: N 29 PHE cc_start: 0.8445 (t80) cc_final: 0.8057 (t80) REVERT: N 38 ARG cc_start: 0.8563 (ptp-170) cc_final: 0.8345 (ptp-170) REVERT: N 39 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: N 126 VAL cc_start: 0.7453 (t) cc_final: 0.7249 (m) REVERT: P 13 TYR cc_start: 0.8365 (t80) cc_final: 0.8017 (t80) REVERT: R 132 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6245 (ttm) REVERT: R 222 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7901 (mp) REVERT: R 240 PHE cc_start: 0.8447 (m-80) cc_final: 0.7841 (m-10) REVERT: R 365 LEU cc_start: 0.8426 (mt) cc_final: 0.8156 (mm) outliers start: 54 outliers final: 36 residues processed: 275 average time/residue: 0.5252 time to fit residues: 154.1488 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 : 0.331 ------------------------------------------------------------------------------- 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 118 ASP 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 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 325 MET Chi-restraints excluded: chain B residue 333 ASP 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 151 ILE 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 256 LEU Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 341 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 74 optimal weight: 0.0010 chunk 71 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 chunk 70 optimal weight: 0.9990 overall best weight: 0.5526 ------------------------------------------------------------------------------- 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 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN R 378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.146195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.125462 restraints weight = 12749.250| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.25 r_work: 0.3497 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8701 Z= 0.145 Angle : 0.586 7.962 11786 Z= 0.302 Chirality : 0.044 0.284 1331 Planarity : 0.005 0.050 1498 Dihedral : 4.522 34.282 1174 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.70 % Allowed : 25.81 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.26), residues: 1062 helix: 1.98 (0.25), residues: 416 sheet: 0.38 (0.33), residues: 225 loop : -0.29 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 134 TYR 0.020 0.001 TYR N 60 PHE 0.021 0.002 PHE R 278 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8697) covalent geometry : angle 0.58557 (11778) SS BOND : bond 0.00316 ( 4) SS BOND : angle 1.14689 ( 8) hydrogen bonds : bond 0.04140 ( 454) hydrogen bonds : angle 4.54708 ( 1296) *********************** 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 312 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7627 (mtm110) cc_final: 0.7013 (mtm110) REVERT: A 31 GLN cc_start: 0.7568 (tp-100) cc_final: 0.7176 (tp40) REVERT: A 34 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7857 (ptmm) REVERT: A 249 ASP cc_start: 0.8044 (t0) cc_final: 0.7778 (t0) REVERT: A 252 ASP cc_start: 0.7938 (t0) cc_final: 0.7566 (t0) REVERT: A 255 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.7941 (mmm-85) REVERT: A 283 LYS cc_start: 0.8670 (mttt) cc_final: 0.8467 (mttt) REVERT: A 320 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: A 337 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7919 (mtm110) REVERT: B 19 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7634 (ttp80) REVERT: B 173 THR cc_start: 0.8422 (m) cc_final: 0.8178 (t) REVERT: B 198 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8344 (mp) REVERT: B 212 ASP cc_start: 0.8155 (t0) cc_final: 0.7870 (t0) REVERT: B 243 THR cc_start: 0.8481 (t) cc_final: 0.8200 (p) REVERT: B 262 MET cc_start: 0.8468 (ttm) cc_final: 0.8173 (ttm) REVERT: B 298 ASP cc_start: 0.7876 (t0) cc_final: 0.7436 (p0) REVERT: B 316 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8135 (p) REVERT: B 325 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7742 (ttp) REVERT: B 333 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.6556 (t0) REVERT: N 21 SER cc_start: 0.8573 (t) cc_final: 0.8182 (p) REVERT: N 29 PHE cc_start: 0.8369 (t80) cc_final: 0.7976 (t80) REVERT: N 39 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: P 13 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.8025 (t80) REVERT: R 132 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.6221 (ttm) REVERT: R 173 MET cc_start: 0.7851 (tpp) cc_final: 0.7438 (mpp) REVERT: R 222 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7898 (mp) REVERT: R 240 PHE cc_start: 0.8437 (m-80) cc_final: 0.7863 (m-10) REVERT: R 365 LEU cc_start: 0.8395 (mt) cc_final: 0.8127 (mm) outliers start: 53 outliers final: 36 residues processed: 278 average time/residue: 0.5263 time to fit residues: 156.2511 Evaluate side-chains 289 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 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 325 MET Chi-restraints excluded: chain B residue 333 ASP 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 13 TYR Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 19 ILE 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 300 MET Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 341 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 95 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 125 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 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 = 0.3905 r_free = 0.3905 target = 0.145521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.124868 restraints weight = 12569.551| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.23 r_work: 0.3495 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8701 Z= 0.168 Angle : 0.613 8.115 11786 Z= 0.314 Chirality : 0.045 0.299 1331 Planarity : 0.005 0.045 1498 Dihedral : 4.548 34.117 1174 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.05 % Allowed : 27.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.26), residues: 1062 helix: 1.97 (0.25), residues: 416 sheet: 0.32 (0.33), residues: 222 loop : -0.30 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 134 TYR 0.021 0.001 TYR N 60 PHE 0.023 0.002 PHE B 335 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8697) covalent geometry : angle 0.61199 (11778) SS BOND : bond 0.00362 ( 4) SS BOND : angle 1.22875 ( 8) hydrogen bonds : bond 0.04224 ( 454) hydrogen bonds : angle 4.58226 ( 1296) *********************** 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 293 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7020 (mtm110) REVERT: A 31 GLN cc_start: 0.7560 (tp-100) cc_final: 0.7171 (tp40) REVERT: A 34 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7864 (ptmm) REVERT: A 214 VAL cc_start: 0.8659 (t) cc_final: 0.8422 (t) REVERT: A 249 ASP cc_start: 0.8068 (t0) cc_final: 0.7820 (t0) REVERT: A 252 ASP cc_start: 0.7929 (t0) cc_final: 0.7560 (t0) REVERT: A 255 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.7950 (mmm-85) REVERT: A 320 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: A 337 ARG cc_start: 0.8134 (ttm-80) cc_final: 0.7922 (mtm110) REVERT: B 19 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7620 (ttp80) REVERT: B 82 TRP cc_start: 0.8470 (m100) cc_final: 0.7919 (m100) REVERT: B 173 THR cc_start: 0.8412 (m) cc_final: 0.8170 (t) REVERT: B 198 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8321 (mp) REVERT: B 212 ASP cc_start: 0.8193 (t0) cc_final: 0.7875 (t0) REVERT: B 243 THR cc_start: 0.8485 (t) cc_final: 0.8212 (p) REVERT: B 262 MET cc_start: 0.8455 (ttm) cc_final: 0.8158 (ttm) REVERT: B 298 ASP cc_start: 0.7833 (t0) cc_final: 0.7408 (p0) REVERT: B 325 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7712 (ttp) REVERT: B 333 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7437 (t0) REVERT: N 21 SER cc_start: 0.8570 (t) cc_final: 0.8158 (p) REVERT: N 29 PHE cc_start: 0.8362 (t80) cc_final: 0.7978 (t80) REVERT: N 39 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: P 13 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7971 (t80) REVERT: R 132 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6209 (ttm) REVERT: R 222 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7903 (mp) REVERT: R 278 PHE cc_start: 0.7947 (t80) cc_final: 0.7731 (t80) REVERT: R 317 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7689 (mm-40) REVERT: R 365 LEU cc_start: 0.8424 (mt) cc_final: 0.8161 (mm) outliers start: 47 outliers final: 31 residues processed: 265 average time/residue: 0.5199 time to fit residues: 147.0155 Evaluate side-chains 277 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 313 ASP Chi-restraints excluded: chain A residue 320 GLU 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 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 263 THR Chi-restraints excluded: chain B residue 316 SER 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 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 13 TYR Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 19 ILE 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 341 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 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 0.0050 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.146432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.125816 restraints weight = 12582.114| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.23 r_work: 0.3510 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8701 Z= 0.131 Angle : 0.592 8.334 11786 Z= 0.304 Chirality : 0.044 0.291 1331 Planarity : 0.004 0.045 1498 Dihedral : 4.452 33.613 1174 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.95 % Allowed : 27.96 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.26), residues: 1062 helix: 2.00 (0.25), residues: 416 sheet: 0.37 (0.34), residues: 222 loop : -0.31 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 134 TYR 0.021 0.001 TYR N 60 PHE 0.017 0.002 PHE R 240 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8697) covalent geometry : angle 0.59180 (11778) SS BOND : bond 0.00264 ( 4) SS BOND : angle 1.09581 ( 8) hydrogen bonds : bond 0.04006 ( 454) hydrogen bonds : angle 4.52858 ( 1296) *********************** 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 293 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 247 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7606 (mtm110) cc_final: 0.6993 (mtm110) REVERT: A 31 GLN cc_start: 0.7555 (tp-100) cc_final: 0.7188 (tp40) REVERT: A 34 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7881 (ptmm) REVERT: A 214 VAL cc_start: 0.8667 (t) cc_final: 0.8450 (t) REVERT: A 249 ASP cc_start: 0.8046 (t0) cc_final: 0.7805 (t0) REVERT: A 252 ASP cc_start: 0.7939 (t0) cc_final: 0.7564 (t0) REVERT: A 255 ARG cc_start: 0.8409 (mmm-85) cc_final: 0.7942 (mmm-85) REVERT: A 320 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: B 19 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7728 (ttp-110) REVERT: B 173 THR cc_start: 0.8431 (m) cc_final: 0.8188 (t) REVERT: B 212 ASP cc_start: 0.8162 (t0) cc_final: 0.7868 (t0) REVERT: B 217 MET cc_start: 0.7674 (pmt) cc_final: 0.7447 (pmm) REVERT: B 243 THR cc_start: 0.8468 (t) cc_final: 0.8178 (p) REVERT: B 262 MET cc_start: 0.8466 (ttm) cc_final: 0.8181 (ttm) REVERT: B 298 ASP cc_start: 0.7812 (t0) cc_final: 0.7463 (p0) REVERT: B 300 LEU cc_start: 0.8327 (mp) cc_final: 0.8049 (mm) REVERT: B 316 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8128 (p) REVERT: B 333 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7338 (t0) REVERT: N 21 SER cc_start: 0.8583 (t) cc_final: 0.8166 (p) REVERT: N 29 PHE cc_start: 0.8325 (t80) cc_final: 0.7975 (t80) REVERT: N 39 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: P 13 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.8008 (t80) REVERT: R 104 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7938 (m110) REVERT: R 132 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.6210 (ttm) REVERT: R 173 MET cc_start: 0.7840 (tpp) cc_final: 0.7418 (mpp) REVERT: R 222 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7911 (mp) REVERT: R 240 PHE cc_start: 0.8401 (m-80) cc_final: 0.7971 (m-10) REVERT: R 278 PHE cc_start: 0.8006 (t80) cc_final: 0.7760 (t80) REVERT: R 365 LEU cc_start: 0.8393 (mt) cc_final: 0.8089 (mm) outliers start: 46 outliers final: 30 residues processed: 265 average time/residue: 0.5101 time to fit residues: 144.6866 Evaluate side-chains 280 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 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 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 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 P residue 19 ILE 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 222 ILE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 372 ILE 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 68 optimal weight: 0.1980 chunk 95 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN N 31 ASN ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126826 restraints weight = 12598.289| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.22 r_work: 0.3515 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8701 Z= 0.137 Angle : 0.614 8.745 11786 Z= 0.312 Chirality : 0.044 0.288 1331 Planarity : 0.005 0.051 1498 Dihedral : 4.442 33.364 1174 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.73 % Allowed : 28.60 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1062 helix: 1.95 (0.25), residues: 417 sheet: 0.37 (0.34), residues: 222 loop : -0.30 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 337 TYR 0.021 0.001 TYR N 60 PHE 0.016 0.002 PHE R 240 TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8697) covalent geometry : angle 0.61336 (11778) SS BOND : bond 0.00264 ( 4) SS BOND : angle 1.08770 ( 8) hydrogen bonds : bond 0.04007 ( 454) hydrogen bonds : angle 4.51419 ( 1296) ********************** 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 284 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7596 (mtm110) cc_final: 0.6980 (mtm110) REVERT: A 31 GLN cc_start: 0.7557 (tp-100) cc_final: 0.7213 (tp40) REVERT: A 34 LYS cc_start: 0.8295 (ptmm) cc_final: 0.7886 (ptmm) REVERT: A 210 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8642 (p) REVERT: A 214 VAL cc_start: 0.8667 (t) cc_final: 0.8431 (t) REVERT: A 249 ASP cc_start: 0.8052 (t0) cc_final: 0.7815 (t0) REVERT: A 252 ASP cc_start: 0.7908 (t0) cc_final: 0.7540 (t0) REVERT: A 255 ARG cc_start: 0.8409 (mmm-85) cc_final: 0.7947 (mmm-85) REVERT: A 320 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: A 346 ARG cc_start: 0.8387 (mmm160) cc_final: 0.8145 (mmm160) REVERT: B 19 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7728 (ttp-110) REVERT: B 173 THR cc_start: 0.8427 (m) cc_final: 0.8171 (t) REVERT: B 212 ASP cc_start: 0.8164 (t0) cc_final: 0.7866 (t0) REVERT: B 243 THR cc_start: 0.8469 (t) cc_final: 0.8187 (p) REVERT: B 262 MET cc_start: 0.8467 (ttm) cc_final: 0.8183 (ttm) REVERT: B 283 ARG cc_start: 0.8457 (tpp80) cc_final: 0.8255 (tpp80) REVERT: B 316 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8135 (p) REVERT: B 333 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7334 (t0) REVERT: N 21 SER cc_start: 0.8593 (t) cc_final: 0.8164 (p) REVERT: N 39 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: P 13 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.7996 (t80) REVERT: R 104 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7934 (m110) REVERT: R 132 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.6220 (ttm) REVERT: R 173 MET cc_start: 0.7819 (tpp) cc_final: 0.7391 (mpp) REVERT: R 222 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7911 (mp) REVERT: R 240 PHE cc_start: 0.8360 (m-80) cc_final: 0.8008 (m-10) REVERT: R 248 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7884 (mtpt) REVERT: R 278 PHE cc_start: 0.7949 (t80) cc_final: 0.7735 (t80) REVERT: R 317 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7691 (mm-40) REVERT: R 365 LEU cc_start: 0.8391 (mt) cc_final: 0.8089 (mm) outliers start: 44 outliers final: 28 residues processed: 262 average time/residue: 0.4924 time to fit residues: 138.1699 Evaluate side-chains 275 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 320 GLU 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 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE 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 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 13 TYR Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 19 ILE 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 222 ILE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 341 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 4 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 0.0020 chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 92 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.126983 restraints weight = 12602.461| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.23 r_work: 0.3511 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8701 Z= 0.141 Angle : 0.613 9.441 11786 Z= 0.314 Chirality : 0.044 0.283 1331 Planarity : 0.005 0.051 1498 Dihedral : 4.441 33.465 1174 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.41 % Allowed : 29.03 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.26), residues: 1062 helix: 1.93 (0.25), residues: 418 sheet: 0.30 (0.34), residues: 224 loop : -0.29 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 337 TYR 0.021 0.001 TYR N 60 PHE 0.016 0.002 PHE R 240 TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8697) covalent geometry : angle 0.61292 (11778) SS BOND : bond 0.00265 ( 4) SS BOND : angle 1.09419 ( 8) hydrogen bonds : bond 0.04008 ( 454) hydrogen bonds : angle 4.52087 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3695.47 seconds wall clock time: 63 minutes 35.75 seconds (3815.75 seconds total)