Starting phenix.real_space_refine on Tue Sep 24 17:04:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xve_38702/09_2024/8xve_38702.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xve_38702/09_2024/8xve_38702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xve_38702/09_2024/8xve_38702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xve_38702/09_2024/8xve_38702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xve_38702/09_2024/8xve_38702.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xve_38702/09_2024/8xve_38702.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5421 2.51 5 N 1474 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8524 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1943 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 430 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 131 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "R" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2459 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.01, per 1000 atoms: 0.59 Number of scatterers: 8524 At special positions: 0 Unit cell: (82.16, 101.92, 146.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1571 8.00 N 1474 7.00 C 5421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.04 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 997.7 milliseconds 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: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 9 through 40 Processing helix chain 'A' and resid 52 through 63 removed outlier: 4.155A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.596A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 302 through 308 removed outlier: 3.537A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 342 removed outlier: 3.739A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.778A pdb=" N LYS B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 13 removed outlier: 4.332A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 25 removed outlier: 4.019A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.531A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 8 through 18 removed outlier: 3.545A pdb=" N VAL P 12 " --> pdb=" O ASP P 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 129 removed outlier: 3.796A pdb=" N ASN R 129 " --> pdb=" O ILE R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 133 Processing helix chain 'R' and resid 134 through 153 removed outlier: 3.828A pdb=" N LEU R 139 " --> pdb=" O GLY R 135 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE R 140 " --> pdb=" O PRO R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 165 removed outlier: 3.795A pdb=" N LEU R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 175 removed outlier: 4.374A pdb=" N MET R 173 " --> pdb=" O PHE R 169 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS R 175 " --> pdb=" O ALA R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 205 Processing helix chain 'R' and resid 215 through 239 removed outlier: 3.565A pdb=" N VAL R 223 " --> pdb=" O ALA R 219 " (cutoff:3.500A) Proline residue: R 235 - end of helix Processing helix chain 'R' and resid 263 through 281 removed outlier: 5.705A pdb=" N ASP R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TRP R 275 " --> pdb=" O THR R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 302 removed outlier: 3.800A pdb=" N PHE R 292 " --> pdb=" O ILE R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 350 Proline residue: R 338 - end of helix removed outlier: 3.542A pdb=" N TYR R 350 " --> pdb=" O LYS R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 390 removed outlier: 3.692A pdb=" N ASN R 373 " --> pdb=" O TYR R 369 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER R 379 " --> pdb=" O ALA R 375 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 390 through 398 removed outlier: 4.813A pdb=" N CYS R 396 " --> pdb=" O ARG R 392 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS R 398 " --> pdb=" O LYS R 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 3.837A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.489A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.562A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.755A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.506A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.827A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.624A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.812A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 6.100A pdb=" N GLY N 16 " --> pdb=" O SER N 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.776A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 240 through 247 454 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 2.51 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.340 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8697 Z= 0.245 Angle : 0.627 10.934 11778 Z= 0.361 Chirality : 0.042 0.163 1331 Planarity : 0.006 0.109 1498 Dihedral : 16.632 88.807 3174 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.65 % Allowed : 26.02 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1062 helix: 1.53 (0.25), residues: 408 sheet: 0.34 (0.33), residues: 231 loop : -0.27 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 47 HIS 0.005 0.001 HIS A 347 PHE 0.021 0.002 PHE R 240 TYR 0.010 0.001 TYR N 95 ARG 0.012 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 277 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7158 (mtm110) cc_final: 0.6919 (mtm110) REVERT: A 252 ASP cc_start: 0.7628 (t0) cc_final: 0.7222 (t0) REVERT: A 279 LEU cc_start: 0.8810 (tp) cc_final: 0.8601 (mt) REVERT: A 357 VAL cc_start: 0.8666 (p) cc_final: 0.8406 (m) REVERT: B 204 CYS cc_start: 0.7895 (m) cc_final: 0.7629 (m) REVERT: B 217 MET cc_start: 0.6847 (ptt) cc_final: 0.6643 (ptp) REVERT: B 262 MET cc_start: 0.8301 (ttm) cc_final: 0.7929 (ttm) REVERT: R 365 LEU cc_start: 0.8549 (mt) cc_final: 0.8344 (mt) outliers start: 6 outliers final: 5 residues processed: 281 average time/residue: 1.0751 time to fit residues: 322.6977 Evaluate side-chains 262 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 257 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 378 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.0010 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 94 optimal weight: 0.6980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 261 ASN A 282 ASN B 119 ASN B 142 HIS B 237 ASN B 266 HIS R 104 ASN R 119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8697 Z= 0.191 Angle : 0.588 7.231 11778 Z= 0.310 Chirality : 0.043 0.213 1331 Planarity : 0.005 0.070 1498 Dihedral : 5.124 37.938 1179 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.27 % Allowed : 21.51 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1062 helix: 1.77 (0.25), residues: 419 sheet: 0.43 (0.33), residues: 229 loop : -0.21 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 41 PHE 0.029 0.002 PHE R 278 TYR 0.015 0.001 TYR N 95 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 264 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7249 (mtm110) cc_final: 0.6867 (mtm110) REVERT: A 34 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7905 (ptmm) REVERT: A 252 ASP cc_start: 0.7656 (t0) cc_final: 0.7229 (t0) REVERT: A 256 LEU cc_start: 0.8484 (mt) cc_final: 0.8250 (mt) REVERT: A 317 GLU cc_start: 0.6980 (mp0) cc_final: 0.5781 (mp0) REVERT: A 320 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 369 CYS cc_start: 0.8465 (m) cc_final: 0.8232 (m) REVERT: B 96 ARG cc_start: 0.7135 (ttp80) cc_final: 0.6902 (ttp80) REVERT: B 217 MET cc_start: 0.6948 (ptt) cc_final: 0.6719 (ptp) REVERT: B 262 MET cc_start: 0.8203 (ttm) cc_final: 0.7888 (ttm) REVERT: B 329 THR cc_start: 0.8660 (m) cc_final: 0.8208 (p) REVERT: B 333 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.6487 (t0) REVERT: N 21 SER cc_start: 0.8375 (t) cc_final: 0.8161 (p) REVERT: N 30 SER cc_start: 0.8708 (m) cc_final: 0.8505 (p) REVERT: R 132 MET cc_start: 0.6153 (OUTLIER) cc_final: 0.5873 (ttm) outliers start: 49 outliers final: 24 residues processed: 279 average time/residue: 1.0437 time to fit residues: 311.9206 Evaluate side-chains 272 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 245 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 372 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 94 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 237 ASN B 259 GLN R 119 ASN R 373 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8697 Z= 0.186 Angle : 0.574 12.603 11778 Z= 0.298 Chirality : 0.043 0.231 1331 Planarity : 0.004 0.060 1498 Dihedral : 4.693 39.577 1174 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.62 % Allowed : 22.69 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1062 helix: 1.87 (0.25), residues: 421 sheet: 0.46 (0.34), residues: 224 loop : -0.24 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 PHE 0.018 0.002 PHE B 335 TYR 0.020 0.001 TYR N 60 ARG 0.006 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 253 time to evaluate : 1.044 Fit side-chains REVERT: A 20 ARG cc_start: 0.7167 (mtm110) cc_final: 0.6769 (mtm110) REVERT: A 31 GLN cc_start: 0.7195 (tp-100) cc_final: 0.6837 (tp40) REVERT: A 34 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7824 (ptmm) REVERT: A 252 ASP cc_start: 0.7654 (t0) cc_final: 0.7317 (t0) REVERT: A 264 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8342 (ttmm) REVERT: A 317 GLU cc_start: 0.7029 (mp0) cc_final: 0.5545 (mp0) REVERT: A 320 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6860 (mt-10) REVERT: A 369 CYS cc_start: 0.8499 (m) cc_final: 0.8256 (m) REVERT: B 19 ARG cc_start: 0.7808 (ttp-110) cc_final: 0.7567 (ttp80) REVERT: B 212 ASP cc_start: 0.7874 (t0) cc_final: 0.7656 (t0) REVERT: B 262 MET cc_start: 0.8196 (ttm) cc_final: 0.7864 (ttm) REVERT: B 325 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7431 (ttp) REVERT: B 333 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7332 (t0) REVERT: N 21 SER cc_start: 0.8502 (t) cc_final: 0.8197 (p) REVERT: R 104 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8218 (m110) REVERT: R 132 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5911 (ttm) REVERT: R 173 MET cc_start: 0.7405 (tpp) cc_final: 0.7056 (mpp) REVERT: R 351 ASN cc_start: 0.7392 (t0) cc_final: 0.6811 (p0) outliers start: 43 outliers final: 25 residues processed: 268 average time/residue: 1.0677 time to fit residues: 305.6844 Evaluate side-chains 280 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 250 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER 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 N residue 96 CYS Chi-restraints excluded: chain R residue 104 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 184 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 317 GLN Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.6980 chunk 71 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 237 ASN R 119 ASN R 373 ASN R 378 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8697 Z= 0.190 Angle : 0.562 9.713 11778 Z= 0.291 Chirality : 0.043 0.219 1331 Planarity : 0.004 0.055 1498 Dihedral : 4.530 36.099 1174 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.48 % Allowed : 23.76 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1062 helix: 2.06 (0.25), residues: 415 sheet: 0.57 (0.34), residues: 222 loop : -0.24 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS B 311 PHE 0.014 0.002 PHE N 108 TYR 0.021 0.001 TYR N 60 ARG 0.008 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 254 time to evaluate : 0.976 Fit side-chains REVERT: A 20 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6579 (mtm110) REVERT: A 31 GLN cc_start: 0.7180 (tp-100) cc_final: 0.6948 (tp40) REVERT: A 252 ASP cc_start: 0.7687 (t0) cc_final: 0.7381 (t0) REVERT: A 264 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8341 (ttmm) REVERT: A 317 GLU cc_start: 0.7022 (mp0) cc_final: 0.5423 (mp0) REVERT: A 320 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6516 (mt-10) REVERT: A 369 CYS cc_start: 0.8506 (m) cc_final: 0.8288 (m) REVERT: B 19 ARG cc_start: 0.7781 (ttp-110) cc_final: 0.7474 (ttp80) REVERT: B 212 ASP cc_start: 0.7926 (t0) cc_final: 0.7627 (t0) REVERT: B 243 THR cc_start: 0.8491 (t) cc_final: 0.8223 (p) REVERT: B 262 MET cc_start: 0.8180 (ttm) cc_final: 0.7856 (ttm) REVERT: B 325 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7230 (ttm) REVERT: B 333 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.6643 (t0) REVERT: B 335 PHE cc_start: 0.7471 (m-80) cc_final: 0.7198 (m-80) REVERT: N 21 SER cc_start: 0.8461 (t) cc_final: 0.8122 (p) REVERT: N 82 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7374 (tp-100) REVERT: R 104 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.8035 (m110) REVERT: R 132 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5830 (ttm) REVERT: R 173 MET cc_start: 0.7363 (tpp) cc_final: 0.7002 (mpp) outliers start: 51 outliers final: 27 residues processed: 269 average time/residue: 1.1112 time to fit residues: 319.1404 Evaluate side-chains 281 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 248 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 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 82 GLN 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 104 ASN Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 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 378 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 90 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 373 ASN R 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8697 Z= 0.224 Angle : 0.566 8.008 11778 Z= 0.294 Chirality : 0.043 0.254 1331 Planarity : 0.004 0.051 1498 Dihedral : 4.530 34.325 1174 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.48 % Allowed : 24.73 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1062 helix: 2.03 (0.25), residues: 415 sheet: 0.52 (0.34), residues: 222 loop : -0.32 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 PHE 0.026 0.002 PHE R 278 TYR 0.020 0.001 TYR N 60 ARG 0.008 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 253 time to evaluate : 1.084 Fit side-chains REVERT: A 20 ARG cc_start: 0.7161 (mtm110) cc_final: 0.6570 (mtm110) REVERT: A 31 GLN cc_start: 0.7269 (tp-100) cc_final: 0.6882 (tp40) REVERT: A 34 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7849 (ptmm) REVERT: A 252 ASP cc_start: 0.7691 (t0) cc_final: 0.7400 (t0) REVERT: A 264 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8331 (ttmm) REVERT: A 317 GLU cc_start: 0.7031 (mp0) cc_final: 0.5387 (mp0) REVERT: A 320 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6483 (mt-10) REVERT: A 369 CYS cc_start: 0.8508 (m) cc_final: 0.8294 (m) REVERT: B 19 ARG cc_start: 0.7809 (ttp-110) cc_final: 0.7520 (ttp80) REVERT: B 212 ASP cc_start: 0.7937 (t0) cc_final: 0.7581 (t0) REVERT: B 243 THR cc_start: 0.8524 (t) cc_final: 0.8246 (p) REVERT: B 262 MET cc_start: 0.8185 (ttm) cc_final: 0.7865 (ttm) REVERT: B 333 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.6554 (t0) REVERT: B 335 PHE cc_start: 0.7527 (m-80) cc_final: 0.7178 (m-80) REVERT: N 21 SER cc_start: 0.8565 (t) cc_final: 0.8057 (p) REVERT: N 29 PHE cc_start: 0.8443 (t80) cc_final: 0.8048 (t80) REVERT: N 39 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: P 13 TYR cc_start: 0.8175 (t80) cc_final: 0.7802 (t80) REVERT: R 132 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5770 (ttm) REVERT: R 158 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7671 (m-40) REVERT: R 173 MET cc_start: 0.7361 (tpp) cc_final: 0.6988 (mpp) REVERT: R 240 PHE cc_start: 0.8373 (m-80) cc_final: 0.7724 (m-10) outliers start: 51 outliers final: 29 residues processed: 269 average time/residue: 1.1328 time to fit residues: 325.3020 Evaluate side-chains 290 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 255 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 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 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 158 ASN Chi-restraints excluded: chain R residue 184 SER Chi-restraints excluded: chain R residue 238 ILE 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 378 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 83 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 237 ASN R 373 ASN R 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8697 Z= 0.211 Angle : 0.584 8.357 11778 Z= 0.301 Chirality : 0.044 0.283 1331 Planarity : 0.004 0.049 1498 Dihedral : 4.487 33.772 1174 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.81 % Allowed : 24.62 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1062 helix: 2.00 (0.25), residues: 417 sheet: 0.52 (0.34), residues: 220 loop : -0.31 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS B 311 PHE 0.015 0.002 PHE N 108 TYR 0.021 0.001 TYR N 60 ARG 0.012 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 252 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6565 (mtm110) REVERT: A 31 GLN cc_start: 0.7242 (tp-100) cc_final: 0.6876 (tp40) REVERT: A 34 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7852 (ptmm) REVERT: A 252 ASP cc_start: 0.7694 (t0) cc_final: 0.7408 (t0) REVERT: A 317 GLU cc_start: 0.7050 (mp0) cc_final: 0.5371 (mp0) REVERT: A 320 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6474 (mt-10) REVERT: A 369 CYS cc_start: 0.8475 (m) cc_final: 0.8266 (m) REVERT: B 19 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.7476 (ttp80) REVERT: B 212 ASP cc_start: 0.7972 (t0) cc_final: 0.7611 (t0) REVERT: B 243 THR cc_start: 0.8517 (t) cc_final: 0.8236 (p) REVERT: B 262 MET cc_start: 0.8183 (ttm) cc_final: 0.7867 (ttm) REVERT: B 316 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8115 (p) REVERT: B 333 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.6479 (t0) REVERT: B 335 PHE cc_start: 0.7487 (m-80) cc_final: 0.7186 (m-80) REVERT: N 21 SER cc_start: 0.8599 (t) cc_final: 0.8123 (p) REVERT: N 29 PHE cc_start: 0.8401 (t80) cc_final: 0.8021 (t80) REVERT: N 39 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: P 13 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7754 (t80) REVERT: R 104 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7944 (m110) REVERT: R 132 MET cc_start: 0.6016 (OUTLIER) cc_final: 0.5699 (ttm) REVERT: R 173 MET cc_start: 0.7345 (tpp) cc_final: 0.6959 (mpp) REVERT: R 222 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7947 (mp) REVERT: R 240 PHE cc_start: 0.8346 (m-80) cc_final: 0.7754 (m-10) REVERT: R 365 LEU cc_start: 0.8382 (mt) cc_final: 0.8080 (mm) outliers start: 54 outliers final: 36 residues processed: 274 average time/residue: 1.0500 time to fit residues: 307.4852 Evaluate side-chains 288 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 243 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 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 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 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 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 158 ASN Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 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 378 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 30.0000 chunk 73 optimal weight: 0.5980 chunk 56 optimal weight: 50.0000 chunk 84 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 125 ASN B 237 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN R 378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8697 Z= 0.224 Angle : 0.579 7.750 11778 Z= 0.301 Chirality : 0.044 0.294 1331 Planarity : 0.004 0.047 1498 Dihedral : 4.496 33.642 1174 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.48 % Allowed : 25.48 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1062 helix: 2.03 (0.25), residues: 416 sheet: 0.51 (0.34), residues: 220 loop : -0.31 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 PHE 0.016 0.002 PHE N 108 TYR 0.021 0.001 TYR N 60 ARG 0.011 0.001 ARG A 337 *********************** 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 297 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 246 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7144 (mtm110) cc_final: 0.6544 (mtm110) REVERT: A 31 GLN cc_start: 0.7220 (tp-100) cc_final: 0.6869 (tp40) REVERT: A 34 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7849 (ptmm) REVERT: A 249 ASP cc_start: 0.7907 (t0) cc_final: 0.7617 (t0) REVERT: A 252 ASP cc_start: 0.7693 (t0) cc_final: 0.7381 (t0) REVERT: A 317 GLU cc_start: 0.7060 (mp0) cc_final: 0.5357 (mp0) REVERT: A 320 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6442 (mt-10) REVERT: A 369 CYS cc_start: 0.8470 (m) cc_final: 0.8267 (m) REVERT: B 19 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7473 (ttp80) REVERT: B 198 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8260 (mp) REVERT: B 243 THR cc_start: 0.8518 (t) cc_final: 0.8236 (p) REVERT: B 262 MET cc_start: 0.8183 (ttm) cc_final: 0.7868 (ttm) REVERT: B 316 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.8136 (p) REVERT: B 333 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.6434 (t0) REVERT: B 335 PHE cc_start: 0.7488 (m-80) cc_final: 0.7153 (m-80) REVERT: N 21 SER cc_start: 0.8550 (t) cc_final: 0.8101 (p) REVERT: N 29 PHE cc_start: 0.8397 (t80) cc_final: 0.8016 (t80) REVERT: N 39 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: P 13 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7728 (t80) REVERT: R 104 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.7959 (m110) REVERT: R 132 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.5766 (ttm) REVERT: R 222 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7948 (mp) REVERT: R 240 PHE cc_start: 0.8299 (m-80) cc_final: 0.7748 (m-10) REVERT: R 365 LEU cc_start: 0.8386 (mt) cc_final: 0.8081 (mm) outliers start: 51 outliers final: 34 residues processed: 268 average time/residue: 1.1266 time to fit residues: 322.6012 Evaluate side-chains 289 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 245 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 251 ARG 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 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 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 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 158 ASN Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 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 378 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 0.0470 chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 237 ASN B 266 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8697 Z= 0.247 Angle : 0.604 8.228 11778 Z= 0.312 Chirality : 0.045 0.298 1331 Planarity : 0.005 0.046 1498 Dihedral : 4.529 34.198 1174 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.38 % Allowed : 26.34 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1062 helix: 2.00 (0.25), residues: 416 sheet: 0.36 (0.33), residues: 222 loop : -0.31 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS B 311 PHE 0.023 0.002 PHE R 278 TYR 0.021 0.001 TYR N 60 ARG 0.012 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 245 time to evaluate : 1.092 Fit side-chains REVERT: A 20 ARG cc_start: 0.7159 (mtm110) cc_final: 0.6550 (mtm110) REVERT: A 31 GLN cc_start: 0.7220 (tp-100) cc_final: 0.6872 (tp40) REVERT: A 34 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7851 (ptmm) REVERT: A 252 ASP cc_start: 0.7701 (t0) cc_final: 0.7433 (t0) REVERT: A 255 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7783 (mmm-85) REVERT: A 317 GLU cc_start: 0.7066 (mp0) cc_final: 0.5323 (mp0) REVERT: A 320 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6380 (mt-10) REVERT: A 369 CYS cc_start: 0.8481 (m) cc_final: 0.8279 (m) REVERT: B 19 ARG cc_start: 0.7781 (ttp-110) cc_final: 0.7417 (ttp80) REVERT: B 198 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 212 ASP cc_start: 0.8011 (t0) cc_final: 0.7608 (t0) REVERT: B 243 THR cc_start: 0.8526 (t) cc_final: 0.8247 (p) REVERT: B 262 MET cc_start: 0.8180 (ttm) cc_final: 0.7868 (ttm) REVERT: B 283 ARG cc_start: 0.8599 (tpt-90) cc_final: 0.8179 (tpp80) REVERT: B 316 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8140 (p) REVERT: B 333 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.6466 (t0) REVERT: B 335 PHE cc_start: 0.7522 (m-80) cc_final: 0.7163 (m-80) REVERT: N 21 SER cc_start: 0.8556 (t) cc_final: 0.8133 (p) REVERT: N 29 PHE cc_start: 0.8403 (t80) cc_final: 0.8029 (t80) REVERT: N 39 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: P 13 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7727 (t80) REVERT: R 104 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7965 (m110) REVERT: R 132 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5778 (ttm) REVERT: R 222 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7945 (mp) REVERT: R 240 PHE cc_start: 0.8276 (m-80) cc_final: 0.7755 (m-10) REVERT: R 365 LEU cc_start: 0.8403 (mt) cc_final: 0.8099 (mm) REVERT: R 368 ASP cc_start: 0.7739 (m-30) cc_final: 0.7500 (m-30) outliers start: 50 outliers final: 34 residues processed: 268 average time/residue: 1.0502 time to fit residues: 300.8922 Evaluate side-chains 283 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 239 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain 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 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 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 158 ASN 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 378 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 119 ASN B 237 ASN B 266 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8697 Z= 0.204 Angle : 0.602 9.784 11778 Z= 0.309 Chirality : 0.044 0.279 1331 Planarity : 0.005 0.045 1498 Dihedral : 4.465 33.707 1174 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.48 % Allowed : 26.67 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1062 helix: 1.99 (0.25), residues: 416 sheet: 0.41 (0.33), residues: 220 loop : -0.34 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 311 PHE 0.014 0.002 PHE N 108 TYR 0.020 0.001 TYR N 60 ARG 0.015 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 247 time to evaluate : 0.927 Fit side-chains REVERT: A 20 ARG cc_start: 0.7126 (mtm110) cc_final: 0.6529 (mtm110) REVERT: A 31 GLN cc_start: 0.7202 (tp-100) cc_final: 0.6858 (tp40) REVERT: A 34 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7853 (ptmm) REVERT: A 249 ASP cc_start: 0.7890 (t0) cc_final: 0.7659 (t0) REVERT: A 252 ASP cc_start: 0.7690 (t0) cc_final: 0.7398 (t0) REVERT: A 255 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7768 (mmm-85) REVERT: A 317 GLU cc_start: 0.7053 (mp0) cc_final: 0.5309 (mp0) REVERT: A 320 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6386 (mt-10) REVERT: B 19 ARG cc_start: 0.7774 (ttp-110) cc_final: 0.7539 (ttp-110) REVERT: B 198 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8225 (mp) REVERT: B 212 ASP cc_start: 0.8002 (t0) cc_final: 0.7600 (t0) REVERT: B 243 THR cc_start: 0.8518 (t) cc_final: 0.8230 (p) REVERT: B 262 MET cc_start: 0.8170 (ttm) cc_final: 0.7882 (ttm) REVERT: B 283 ARG cc_start: 0.8587 (tpt-90) cc_final: 0.8081 (tpp80) REVERT: B 316 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8130 (p) REVERT: B 333 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.6430 (t0) REVERT: N 21 SER cc_start: 0.8565 (t) cc_final: 0.8149 (p) REVERT: N 29 PHE cc_start: 0.8388 (t80) cc_final: 0.8010 (t80) REVERT: N 39 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: P 13 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7746 (t80) REVERT: R 104 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.7975 (m110) REVERT: R 132 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5773 (ttm) REVERT: R 222 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7944 (mp) REVERT: R 240 PHE cc_start: 0.8256 (m-80) cc_final: 0.7746 (m-10) REVERT: R 278 PHE cc_start: 0.7826 (t80) cc_final: 0.7578 (t80) REVERT: R 365 LEU cc_start: 0.8380 (mt) cc_final: 0.8086 (mm) REVERT: R 368 ASP cc_start: 0.7730 (m-30) cc_final: 0.7456 (m-30) outliers start: 51 outliers final: 34 residues processed: 272 average time/residue: 1.0189 time to fit residues: 296.6113 Evaluate side-chains 287 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 243 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 47 THR Chi-restraints excluded: chain B residue 55 LEU 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 251 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain 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 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 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 158 ASN 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 46 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 0.0050 chunk 8 optimal weight: 0.3980 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 87 optimal weight: 0.1980 chunk 25 optimal weight: 9.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 266 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8697 Z= 0.177 Angle : 0.610 10.024 11778 Z= 0.311 Chirality : 0.044 0.286 1331 Planarity : 0.005 0.053 1498 Dihedral : 4.391 34.301 1174 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.73 % Allowed : 28.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1062 helix: 1.92 (0.25), residues: 418 sheet: 0.42 (0.34), residues: 220 loop : -0.29 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 PHE 0.018 0.001 PHE B 335 TYR 0.021 0.001 TYR N 60 ARG 0.014 0.001 ARG A 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 247 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7105 (mtm110) cc_final: 0.6509 (mtm110) REVERT: A 31 GLN cc_start: 0.7187 (tp-100) cc_final: 0.6886 (tp40) REVERT: A 34 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7942 (ptmm) REVERT: A 214 VAL cc_start: 0.8606 (t) cc_final: 0.8385 (t) REVERT: A 249 ASP cc_start: 0.7875 (t0) cc_final: 0.7628 (t0) REVERT: A 252 ASP cc_start: 0.7684 (t0) cc_final: 0.7373 (t0) REVERT: A 320 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7228 (mt-10) REVERT: B 19 ARG cc_start: 0.7742 (ttp-110) cc_final: 0.7368 (ttp80) REVERT: B 198 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8257 (mp) REVERT: B 212 ASP cc_start: 0.7984 (t0) cc_final: 0.7586 (t0) REVERT: B 243 THR cc_start: 0.8503 (t) cc_final: 0.8206 (p) REVERT: B 256 ARG cc_start: 0.8012 (mpp80) cc_final: 0.7505 (mtt180) REVERT: B 262 MET cc_start: 0.8159 (ttm) cc_final: 0.7872 (ttm) REVERT: B 283 ARG cc_start: 0.8564 (tpt-90) cc_final: 0.8092 (tpp80) REVERT: B 316 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8101 (p) REVERT: B 318 LEU cc_start: 0.8486 (tp) cc_final: 0.8173 (tp) REVERT: B 333 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7352 (t0) REVERT: N 21 SER cc_start: 0.8577 (t) cc_final: 0.8162 (p) REVERT: N 29 PHE cc_start: 0.8352 (t80) cc_final: 0.7963 (t80) REVERT: N 39 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: P 13 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7801 (t80) REVERT: R 104 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7967 (m110) REVERT: R 173 MET cc_start: 0.7311 (tpp) cc_final: 0.6902 (mpp) REVERT: R 240 PHE cc_start: 0.8258 (m-80) cc_final: 0.7806 (m-10) REVERT: R 278 PHE cc_start: 0.7821 (t80) cc_final: 0.7434 (t80) REVERT: R 317 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7566 (mm-40) REVERT: R 365 LEU cc_start: 0.8362 (mt) cc_final: 0.8035 (mm) REVERT: R 368 ASP cc_start: 0.7725 (m-30) cc_final: 0.7453 (m-30) outliers start: 44 outliers final: 30 residues processed: 268 average time/residue: 1.0372 time to fit residues: 297.5198 Evaluate side-chains 282 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 244 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 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 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 148 LEU Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 158 ASN 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 76 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 0.0670 chunk 4 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 261 ASN B 237 ASN B 266 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.148036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127116 restraints weight = 12486.296| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.25 r_work: 0.3510 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8697 Z= 0.217 Angle : 0.615 11.546 11778 Z= 0.317 Chirality : 0.045 0.287 1331 Planarity : 0.005 0.052 1498 Dihedral : 4.436 33.669 1174 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.73 % Allowed : 28.28 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1062 helix: 1.90 (0.25), residues: 417 sheet: 0.43 (0.34), residues: 220 loop : -0.29 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 PHE 0.018 0.002 PHE B 335 TYR 0.018 0.001 TYR N 60 ARG 0.014 0.001 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4783.17 seconds wall clock time: 83 minutes 41.45 seconds (5021.45 seconds total)