Starting phenix.real_space_refine on Sun Apr 5 06:26:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vo2_65222/04_2026/9vo2_65222.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vo2_65222/04_2026/9vo2_65222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vo2_65222/04_2026/9vo2_65222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vo2_65222/04_2026/9vo2_65222.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vo2_65222/04_2026/9vo2_65222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vo2_65222/04_2026/9vo2_65222.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.761 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 57 5.16 5 C 5506 2.51 5 N 1468 2.21 5 O 1558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8589 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1790 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2476 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2251 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "S" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1719 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Time building chain proxies: 2.03, per 1000 atoms: 0.24 Number of scatterers: 8589 At special positions: 0 Unit cell: (86.92, 119.72, 124.64, 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 57 16.00 O 1558 8.00 N 1468 7.00 C 5506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 1.02 Conformation dependent library (CDL) restraints added in 382.9 milliseconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 38.7% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.776A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.692A pdb=" N PHE A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.552A pdb=" N ARG A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 28 through 62 removed outlier: 4.116A pdb=" N LEU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) Proline residue: R 37 - end of helix Proline residue: R 49 - end of helix removed outlier: 3.785A pdb=" N MET R 62 " --> pdb=" O TYR R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 95 Proline residue: R 87 - end of helix Processing helix chain 'R' and resid 101 through 137 removed outlier: 4.180A pdb=" N MET R 105 " --> pdb=" O PHE R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 145 Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.807A pdb=" N ALA R 150 " --> pdb=" O LYS R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 172 removed outlier: 4.206A pdb=" N PHE R 170 " --> pdb=" O ILE R 166 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU R 171 " --> pdb=" O PRO R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 207 Processing helix chain 'R' and resid 207 through 227 Processing helix chain 'R' and resid 233 through 270 Proline residue: R 256 - end of helix removed outlier: 3.586A pdb=" N LEU R 269 " --> pdb=" O ILE R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 293 Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 293 through 303 Processing helix chain 'R' and resid 306 through 320 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.387A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.291A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 254 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N HIS A 327 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 256 " --> pdb=" O HIS A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.538A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.618A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.082A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.606A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.838A 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: 3.860A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.295A 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: 6.476A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.592A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.598A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.069A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.908A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1362 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.32 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: 2749 1.34 - 1.46: 2134 1.46 - 1.58: 3818 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8779 Sorted by residual: bond pdb=" CG1 ILE A 243 " pdb=" CD1 ILE A 243 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.07e+00 bond pdb=" N ILE G 28 " pdb=" CA ILE G 28 " ideal model delta sigma weight residual 1.459 1.440 0.019 1.25e-02 6.40e+03 2.41e+00 bond pdb=" CA ARG R 288 " pdb=" C ARG R 288 " ideal model delta sigma weight residual 1.520 1.538 -0.018 1.23e-02 6.61e+03 2.15e+00 bond pdb=" C PRO A 291 " pdb=" N GLU A 292 " ideal model delta sigma weight residual 1.329 1.309 0.020 1.60e-02 3.91e+03 1.53e+00 bond pdb=" CG PRO R 64 " pdb=" CD PRO R 64 " ideal model delta sigma weight residual 1.512 1.480 0.032 2.70e-02 1.37e+03 1.41e+00 ... (remaining 8774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 11642 2.03 - 4.06: 270 4.06 - 6.10: 33 6.10 - 8.13: 8 8.13 - 10.16: 2 Bond angle restraints: 11955 Sorted by residual: angle pdb=" CA PRO R 210 " pdb=" N PRO R 210 " pdb=" CD PRO R 210 " ideal model delta sigma weight residual 112.00 107.47 4.53 1.40e+00 5.10e-01 1.05e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 122.23 117.29 4.94 1.57e+00 4.06e-01 9.90e+00 angle pdb=" N GLU S 89 " pdb=" CA GLU S 89 " pdb=" C GLU S 89 " ideal model delta sigma weight residual 114.64 109.98 4.66 1.52e+00 4.33e-01 9.40e+00 angle pdb=" C PRO A 291 " pdb=" N GLU A 292 " pdb=" CA GLU A 292 " ideal model delta sigma weight residual 120.49 116.15 4.34 1.42e+00 4.96e-01 9.32e+00 ... (remaining 11950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4792 17.98 - 35.97: 311 35.97 - 53.95: 30 53.95 - 71.94: 11 71.94 - 89.92: 5 Dihedral angle restraints: 5149 sinusoidal: 1815 harmonic: 3334 Sorted by residual: dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 153.50 26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA THR A 329 " pdb=" C THR A 329 " pdb=" N CYS A 330 " pdb=" CA CYS A 330 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1072 0.057 - 0.114: 285 0.114 - 0.171: 41 0.171 - 0.228: 1 0.228 - 0.284: 1 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CG LEU B 95 " pdb=" CB LEU B 95 " pdb=" CD1 LEU B 95 " pdb=" CD2 LEU B 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CA VAL S 37 " pdb=" N VAL S 37 " pdb=" C VAL S 37 " pdb=" CB VAL S 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 1397 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 209 " 0.078 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO R 210 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO R 210 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO R 210 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 290 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO A 291 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 277 " 0.065 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A 278 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 278 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 278 " 0.052 5.00e-02 4.00e+02 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 139 2.67 - 3.23: 8075 3.23 - 3.79: 13803 3.79 - 4.34: 19431 4.34 - 4.90: 32310 Nonbonded interactions: 73758 Sorted by model distance: nonbonded pdb=" OH TYR A 325 " pdb=" OD2 ASP A 346 " model vdw 2.116 3.040 nonbonded pdb=" OH TYR R 118 " pdb=" NH2 ARG R 261 " model vdw 2.134 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.163 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.172 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.182 3.120 ... (remaining 73753 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: 1.800 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.220 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 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 : 0.005 0.068 8781 Z= 0.229 Angle : 0.769 10.160 11959 Z= 0.431 Chirality : 0.050 0.284 1400 Planarity : 0.008 0.116 1505 Dihedral : 12.269 89.919 2987 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1127 helix: 1.18 (0.24), residues: 405 sheet: 0.75 (0.29), residues: 275 loop : -0.87 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 131 TYR 0.021 0.002 TYR S 178 PHE 0.047 0.003 PHE R 127 TRP 0.035 0.003 TRP B 211 HIS 0.020 0.003 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 8779) covalent geometry : angle 0.76774 (11955) SS BOND : bond 0.00534 ( 2) SS BOND : angle 2.60797 ( 4) hydrogen bonds : bond 0.11781 ( 473) hydrogen bonds : angle 6.07337 ( 1362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.253 Fit side-chains REVERT: A 304 TYR cc_start: 0.8846 (m-80) cc_final: 0.8550 (m-80) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.6274 time to fit residues: 96.9090 Evaluate side-chains 125 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 278 ASN R 294 ASN S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.044262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2309 r_free = 0.2309 target = 0.039872 restraints weight = 21182.570| |-----------------------------------------------------------------------------| r_work (start): 0.2309 rms_B_bonded: 1.10 r_work: 0.2238 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2164 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8781 Z= 0.153 Angle : 0.614 6.622 11959 Z= 0.331 Chirality : 0.044 0.206 1400 Planarity : 0.006 0.079 1505 Dihedral : 5.027 26.613 1227 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.06 % Allowed : 6.30 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1127 helix: 1.71 (0.24), residues: 417 sheet: 0.61 (0.29), residues: 274 loop : -0.67 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.016 0.002 TYR S 178 PHE 0.023 0.002 PHE R 127 TRP 0.020 0.002 TRP B 82 HIS 0.009 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8779) covalent geometry : angle 0.61337 (11955) SS BOND : bond 0.00460 ( 2) SS BOND : angle 1.65400 ( 4) hydrogen bonds : bond 0.04696 ( 473) hydrogen bonds : angle 5.01288 ( 1362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.405 Fit side-chains REVERT: B 258 ASP cc_start: 0.8898 (t70) cc_final: 0.8664 (t0) REVERT: B 325 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8272 (mmm) REVERT: R 66 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8648 (mtpp) outliers start: 18 outliers final: 5 residues processed: 147 average time/residue: 0.6349 time to fit residues: 98.7519 Evaluate side-chains 138 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 42 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 259 ASN A 322 HIS R 294 ASN S 82 GLN S 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.044782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2322 r_free = 0.2322 target = 0.040391 restraints weight = 21025.228| |-----------------------------------------------------------------------------| r_work (start): 0.2321 rms_B_bonded: 1.09 r_work: 0.2251 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2178 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8781 Z= 0.134 Angle : 0.558 6.188 11959 Z= 0.301 Chirality : 0.042 0.158 1400 Planarity : 0.005 0.069 1505 Dihedral : 4.722 25.863 1227 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.52 % Allowed : 7.56 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.25), residues: 1127 helix: 2.23 (0.25), residues: 412 sheet: 0.72 (0.29), residues: 279 loop : -0.64 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 134 TYR 0.014 0.001 TYR S 178 PHE 0.015 0.002 PHE A 189 TRP 0.017 0.002 TRP A 211 HIS 0.007 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8779) covalent geometry : angle 0.55783 (11955) SS BOND : bond 0.00400 ( 2) SS BOND : angle 1.21797 ( 4) hydrogen bonds : bond 0.04315 ( 473) hydrogen bonds : angle 4.76341 ( 1362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.341 Fit side-chains REVERT: A 28 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: A 343 ASP cc_start: 0.8422 (m-30) cc_final: 0.8123 (m-30) REVERT: B 258 ASP cc_start: 0.8842 (t70) cc_final: 0.8494 (t0) REVERT: R 66 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8663 (mtpp) outliers start: 22 outliers final: 5 residues processed: 142 average time/residue: 0.6572 time to fit residues: 98.4534 Evaluate side-chains 137 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain S residue 138 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN R 294 ASN S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.042109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2243 r_free = 0.2243 target = 0.037720 restraints weight = 21253.536| |-----------------------------------------------------------------------------| r_work (start): 0.2243 rms_B_bonded: 1.07 r_work: 0.2171 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2097 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.2097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8781 Z= 0.199 Angle : 0.628 6.982 11959 Z= 0.338 Chirality : 0.044 0.171 1400 Planarity : 0.005 0.065 1505 Dihedral : 4.986 26.700 1227 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.75 % Allowed : 10.08 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.25), residues: 1127 helix: 2.21 (0.25), residues: 411 sheet: 0.77 (0.30), residues: 278 loop : -0.70 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 134 TYR 0.013 0.002 TYR A 356 PHE 0.018 0.002 PHE R 207 TRP 0.019 0.002 TRP B 82 HIS 0.014 0.002 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8779) covalent geometry : angle 0.62760 (11955) SS BOND : bond 0.00539 ( 2) SS BOND : angle 1.56330 ( 4) hydrogen bonds : bond 0.04907 ( 473) hydrogen bonds : angle 4.96422 ( 1362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.341 Fit side-chains REVERT: A 28 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.7783 (mt0) REVERT: A 304 TYR cc_start: 0.9149 (m-80) cc_final: 0.8846 (m-80) REVERT: B 325 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8352 (mmm) REVERT: R 66 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8690 (mtpp) outliers start: 24 outliers final: 12 residues processed: 144 average time/residue: 0.6651 time to fit residues: 101.0272 Evaluate side-chains 149 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN R 294 ASN S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.042655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2260 r_free = 0.2260 target = 0.038284 restraints weight = 21059.446| |-----------------------------------------------------------------------------| r_work (start): 0.2259 rms_B_bonded: 1.08 r_work: 0.2188 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2113 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8781 Z= 0.164 Angle : 0.580 6.544 11959 Z= 0.314 Chirality : 0.043 0.139 1400 Planarity : 0.005 0.064 1505 Dihedral : 4.860 26.887 1227 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.29 % Allowed : 10.77 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.25), residues: 1127 helix: 2.28 (0.25), residues: 411 sheet: 0.76 (0.29), residues: 278 loop : -0.65 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.014 0.002 TYR S 178 PHE 0.016 0.002 PHE R 207 TRP 0.017 0.002 TRP B 82 HIS 0.010 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8779) covalent geometry : angle 0.57942 (11955) SS BOND : bond 0.00486 ( 2) SS BOND : angle 1.31299 ( 4) hydrogen bonds : bond 0.04581 ( 473) hydrogen bonds : angle 4.84990 ( 1362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.332 Fit side-chains REVERT: A 28 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.7794 (mt0) REVERT: A 233 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8588 (tt) REVERT: B 59 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8325 (m-80) REVERT: B 325 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8298 (mmm) REVERT: G 22 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: G 28 ILE cc_start: 0.8919 (pt) cc_final: 0.8668 (pt) REVERT: R 66 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8671 (mtpp) outliers start: 20 outliers final: 12 residues processed: 145 average time/residue: 0.6518 time to fit residues: 99.7355 Evaluate side-chains 152 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 138 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN R 294 ASN S 171 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.043463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2284 r_free = 0.2284 target = 0.039091 restraints weight = 20606.039| |-----------------------------------------------------------------------------| r_work (start): 0.2283 rms_B_bonded: 1.07 r_work: 0.2212 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2136 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8781 Z= 0.138 Angle : 0.547 6.296 11959 Z= 0.295 Chirality : 0.042 0.140 1400 Planarity : 0.005 0.061 1505 Dihedral : 4.683 26.184 1227 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.75 % Allowed : 11.23 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1127 helix: 2.41 (0.25), residues: 411 sheet: 0.74 (0.29), residues: 281 loop : -0.59 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 134 TYR 0.014 0.001 TYR S 178 PHE 0.016 0.002 PHE A 189 TRP 0.016 0.002 TRP B 169 HIS 0.008 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8779) covalent geometry : angle 0.54704 (11955) SS BOND : bond 0.00432 ( 2) SS BOND : angle 1.15831 ( 4) hydrogen bonds : bond 0.04280 ( 473) hydrogen bonds : angle 4.72864 ( 1362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.324 Fit side-chains REVERT: A 28 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: A 233 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8530 (tt) REVERT: A 343 ASP cc_start: 0.8347 (m-30) cc_final: 0.8034 (m-30) REVERT: B 59 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: B 258 ASP cc_start: 0.8673 (t0) cc_final: 0.8413 (t0) REVERT: B 325 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8283 (mmm) REVERT: G 28 ILE cc_start: 0.8898 (pt) cc_final: 0.8639 (pt) REVERT: R 66 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8673 (mtpp) outliers start: 24 outliers final: 14 residues processed: 147 average time/residue: 0.6900 time to fit residues: 106.9934 Evaluate side-chains 155 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 138 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 62 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN R 294 ASN S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.043936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2295 r_free = 0.2295 target = 0.039490 restraints weight = 20598.496| |-----------------------------------------------------------------------------| r_work (start): 0.2291 rms_B_bonded: 1.10 r_work: 0.2220 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2145 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 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 0.035 8781 Z= 0.132 Angle : 0.537 5.922 11959 Z= 0.290 Chirality : 0.041 0.139 1400 Planarity : 0.004 0.061 1505 Dihedral : 4.587 25.893 1227 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.86 % Allowed : 11.00 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.25), residues: 1127 helix: 2.51 (0.25), residues: 411 sheet: 0.78 (0.29), residues: 281 loop : -0.54 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 134 TYR 0.014 0.001 TYR S 178 PHE 0.016 0.002 PHE A 189 TRP 0.015 0.002 TRP B 169 HIS 0.007 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8779) covalent geometry : angle 0.53637 (11955) SS BOND : bond 0.00417 ( 2) SS BOND : angle 1.07015 ( 4) hydrogen bonds : bond 0.04143 ( 473) hydrogen bonds : angle 4.63378 ( 1362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.352 Fit side-chains REVERT: A 28 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: B 234 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8837 (m-80) REVERT: B 258 ASP cc_start: 0.8579 (t0) cc_final: 0.8352 (t0) REVERT: B 325 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8295 (mmm) REVERT: G 28 ILE cc_start: 0.8887 (pt) cc_final: 0.8637 (pt) REVERT: R 66 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8673 (mtpp) outliers start: 25 outliers final: 12 residues processed: 147 average time/residue: 0.6620 time to fit residues: 102.9680 Evaluate side-chains 149 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 138 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 294 ASN S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2327 r_free = 0.2327 target = 0.040382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2192 r_free = 0.2192 target = 0.036052 restraints weight = 21127.496| |-----------------------------------------------------------------------------| r_work (start): 0.2192 rms_B_bonded: 1.06 r_work: 0.2121 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2045 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8781 Z= 0.261 Angle : 0.692 7.459 11959 Z= 0.370 Chirality : 0.047 0.165 1400 Planarity : 0.005 0.061 1505 Dihedral : 5.136 27.622 1227 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.75 % Allowed : 11.80 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.25), residues: 1127 helix: 2.15 (0.24), residues: 411 sheet: 0.82 (0.30), residues: 280 loop : -0.62 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 134 TYR 0.015 0.002 TYR A 356 PHE 0.018 0.003 PHE R 207 TRP 0.019 0.003 TRP B 82 HIS 0.014 0.002 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00614 ( 8779) covalent geometry : angle 0.69117 (11955) SS BOND : bond 0.00667 ( 2) SS BOND : angle 1.89006 ( 4) hydrogen bonds : bond 0.05309 ( 473) hydrogen bonds : angle 5.06439 ( 1362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.300 Fit side-chains REVERT: A 28 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: A 186 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: A 229 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8827 (m-30) REVERT: A 304 TYR cc_start: 0.9205 (m-80) cc_final: 0.8936 (m-80) REVERT: B 59 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8371 (m-80) REVERT: B 234 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8762 (m-80) REVERT: B 258 ASP cc_start: 0.8803 (t0) cc_final: 0.8584 (t0) REVERT: B 325 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8338 (mmm) REVERT: R 66 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8707 (mtpp) outliers start: 24 outliers final: 14 residues processed: 144 average time/residue: 0.6183 time to fit residues: 94.3182 Evaluate side-chains 156 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 138 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN R 294 ASN S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.042432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2252 r_free = 0.2252 target = 0.038013 restraints weight = 20436.520| |-----------------------------------------------------------------------------| r_work (start): 0.2250 rms_B_bonded: 1.10 r_work: 0.2176 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2100 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8781 Z= 0.159 Angle : 0.583 6.570 11959 Z= 0.314 Chirality : 0.042 0.138 1400 Planarity : 0.005 0.061 1505 Dihedral : 4.870 27.120 1227 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.52 % Allowed : 12.14 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1127 helix: 2.35 (0.24), residues: 410 sheet: 0.77 (0.29), residues: 279 loop : -0.52 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 134 TYR 0.014 0.002 TYR S 178 PHE 0.017 0.002 PHE A 189 TRP 0.016 0.002 TRP R 197 HIS 0.009 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8779) covalent geometry : angle 0.58253 (11955) SS BOND : bond 0.00504 ( 2) SS BOND : angle 1.35667 ( 4) hydrogen bonds : bond 0.04514 ( 473) hydrogen bonds : angle 4.81892 ( 1362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.407 Fit side-chains REVERT: A 28 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: A 186 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: A 229 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8791 (m-30) REVERT: A 304 TYR cc_start: 0.9153 (m-80) cc_final: 0.8871 (m-80) REVERT: B 59 TYR cc_start: 0.9179 (OUTLIER) cc_final: 0.8461 (m-80) REVERT: B 234 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8809 (m-80) REVERT: B 258 ASP cc_start: 0.8691 (t0) cc_final: 0.8430 (t0) REVERT: B 325 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8283 (mmm) REVERT: R 66 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8683 (mtpp) REVERT: S 234 GLU cc_start: 0.8286 (pm20) cc_final: 0.8055 (pm20) outliers start: 22 outliers final: 14 residues processed: 143 average time/residue: 0.6493 time to fit residues: 98.1496 Evaluate side-chains 155 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 138 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 261 GLN R 294 ASN S 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.043106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2273 r_free = 0.2273 target = 0.038688 restraints weight = 20572.493| |-----------------------------------------------------------------------------| r_work (start): 0.2269 rms_B_bonded: 1.10 r_work: 0.2196 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2121 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8781 Z= 0.145 Angle : 0.569 7.578 11959 Z= 0.305 Chirality : 0.042 0.137 1400 Planarity : 0.005 0.061 1505 Dihedral : 4.729 26.309 1227 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.75 % Allowed : 12.37 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1127 helix: 2.44 (0.25), residues: 411 sheet: 0.76 (0.29), residues: 282 loop : -0.50 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 134 TYR 0.015 0.002 TYR S 178 PHE 0.016 0.002 PHE A 189 TRP 0.016 0.002 TRP B 169 HIS 0.008 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8779) covalent geometry : angle 0.56898 (11955) SS BOND : bond 0.00442 ( 2) SS BOND : angle 1.24159 ( 4) hydrogen bonds : bond 0.04329 ( 473) hydrogen bonds : angle 4.72869 ( 1362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.356 Fit side-chains REVERT: A 28 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.7734 (mt0) REVERT: B 59 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: B 234 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8788 (m-80) REVERT: B 325 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8293 (mmm) REVERT: R 66 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8674 (mtpp) REVERT: S 234 GLU cc_start: 0.8302 (pm20) cc_final: 0.8081 (pm20) outliers start: 24 outliers final: 15 residues processed: 147 average time/residue: 0.6439 time to fit residues: 100.1677 Evaluate side-chains 156 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 138 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 60 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 61 optimal weight: 0.0010 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 294 ASN S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.043682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2289 r_free = 0.2289 target = 0.039239 restraints weight = 20590.015| |-----------------------------------------------------------------------------| r_work (start): 0.2289 rms_B_bonded: 1.11 r_work: 0.2217 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2141 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8781 Z= 0.136 Angle : 0.548 6.116 11959 Z= 0.295 Chirality : 0.041 0.139 1400 Planarity : 0.005 0.061 1505 Dihedral : 4.633 26.034 1227 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.63 % Allowed : 12.37 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1127 helix: 2.53 (0.25), residues: 411 sheet: 0.75 (0.29), residues: 282 loop : -0.45 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 134 TYR 0.015 0.001 TYR S 178 PHE 0.016 0.002 PHE A 189 TRP 0.016 0.002 TRP B 169 HIS 0.007 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8779) covalent geometry : angle 0.54740 (11955) SS BOND : bond 0.00425 ( 2) SS BOND : angle 1.15828 ( 4) hydrogen bonds : bond 0.04204 ( 473) hydrogen bonds : angle 4.66783 ( 1362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3077.36 seconds wall clock time: 53 minutes 23.29 seconds (3203.29 seconds total)