Starting phenix.real_space_refine on Tue May 13 10:28:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ct3_45897/05_2025/9ct3_45897.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ct3_45897/05_2025/9ct3_45897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ct3_45897/05_2025/9ct3_45897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ct3_45897/05_2025/9ct3_45897.map" model { file = "/net/cci-nas-00/data/ceres_data/9ct3_45897/05_2025/9ct3_45897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ct3_45897/05_2025/9ct3_45897.cif" } resolution = 3.09 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= 0.024 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: 6 Type Number sf(0) Gaussians S 52 5.16 5 Cl 2 4.86 5 C 6508 2.51 5 N 1772 2.21 5 O 1788 1.98 5 F 16 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10138 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2508 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 18, 'TRANS': 300} Chain breaks: 2 Chain: "B" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2477 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 17, 'TRANS': 296} Chain breaks: 3 Chain: "C" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2508 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 18, 'TRANS': 300} Chain breaks: 2 Chain: "D" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2477 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 17, 'TRANS': 296} Chain breaks: 3 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'9IM': 1, 'V67': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'V67': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'9IM': 1, 'V67': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'V67': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.42, per 1000 atoms: 0.63 Number of scatterers: 10138 At special positions: 0 Unit cell: (104.11, 91.186, 104.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 52 16.00 F 16 9.00 O 1788 8.00 N 1772 7.00 C 6508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 64.8% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 Processing helix chain 'A' and resid 39 through 70 removed outlier: 3.786A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 80 through 90 removed outlier: 3.677A pdb=" N THR A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 108 Processing helix chain 'A' and resid 116 through 134 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.696A pdb=" N GLY A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 185 Proline residue: A 173 - end of helix removed outlier: 4.358A pdb=" N GLN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ALA A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 262 through 274 removed outlier: 3.678A pdb=" N GLN A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 302 Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.610A pdb=" N GLU A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 37 removed outlier: 3.757A pdb=" N GLY B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 70 removed outlier: 3.749A pdb=" N THR B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'B' and resid 91 through 109 Processing helix chain 'B' and resid 117 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 154 through 167 removed outlier: 3.566A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 Proline residue: B 173 - end of helix removed outlier: 4.465A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 262 through 274 removed outlier: 3.501A pdb=" N GLN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 302 removed outlier: 3.775A pdb=" N ASP B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 333 Processing helix chain 'C' and resid 16 through 37 removed outlier: 3.663A pdb=" N GLY C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 70 removed outlier: 3.782A pdb=" N GLU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.539A pdb=" N THR C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 108 Processing helix chain 'C' and resid 116 through 134 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 154 through 167 removed outlier: 3.670A pdb=" N GLY C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 186 Proline residue: C 173 - end of helix removed outlier: 4.341A pdb=" N GLN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA C 177 " --> pdb=" O PRO C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 Processing helix chain 'C' and resid 262 through 274 removed outlier: 3.604A pdb=" N GLN C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 302 Processing helix chain 'C' and resid 324 through 333 removed outlier: 3.601A pdb=" N GLU C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 36 Processing helix chain 'D' and resid 39 through 70 removed outlier: 3.787A pdb=" N THR D 43 " --> pdb=" O PRO D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 80 through 90 removed outlier: 3.566A pdb=" N THR D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 109 Processing helix chain 'D' and resid 117 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 154 through 167 removed outlier: 3.526A pdb=" N GLY D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 186 Proline residue: D 173 - end of helix Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'D' and resid 262 through 274 removed outlier: 3.579A pdb=" N GLN D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.647A pdb=" N ASP D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 224 removed outlier: 6.236A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU A 248 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE A 221 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU A 246 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 223 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SER A 243 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 259 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU A 249 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 232 removed outlier: 6.821A pdb=" N HIS A 232 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LYS A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 224 removed outlier: 6.810A pdb=" N ILE B 244 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER B 243 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL B 258 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR B 245 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR B 256 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 247 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 228 through 230 Processing sheet with id=AA5, first strand: chain 'C' and resid 219 through 224 removed outlier: 6.227A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU C 248 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N PHE C 221 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU C 246 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N SER C 243 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU C 259 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY C 255 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU C 249 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ARG C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N SER C 195 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR C 256 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ARG C 197 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL C 258 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 260 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ARG C 310 " --> pdb=" O GLN C 196 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU C 198 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 312 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 200 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N TYR C 314 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C 202 " --> pdb=" O TYR C 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 228 through 232 removed outlier: 6.794A pdb=" N HIS C 232 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LYS C 236 " --> pdb=" O HIS C 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 219 through 224 removed outlier: 6.882A pdb=" N ILE D 244 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER D 243 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU D 259 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU D 249 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ARG D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 228 through 230 643 hydrogen bonds defined for protein. 1890 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: 2.95 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1592 1.31 - 1.43: 2884 1.43 - 1.56: 5838 1.56 - 1.68: 0 1.68 - 1.81: 66 Bond restraints: 10380 Sorted by residual: bond pdb=" C16 9IM A 402 " pdb=" N06 9IM A 402 " ideal model delta sigma weight residual 1.393 1.528 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C16 9IM C 402 " pdb=" N06 9IM C 402 " ideal model delta sigma weight residual 1.393 1.525 -0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" C8 V67 B 401 " pdb=" N10 V67 B 401 " ideal model delta sigma weight residual 1.343 1.455 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C8 V67 D 401 " pdb=" N10 V67 D 401 " ideal model delta sigma weight residual 1.343 1.455 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C8 V67 A 401 " pdb=" N10 V67 A 401 " ideal model delta sigma weight residual 1.343 1.454 -0.111 2.00e-02 2.50e+03 3.08e+01 ... (remaining 10375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 14039 3.66 - 7.31: 63 7.31 - 10.97: 4 10.97 - 14.62: 8 14.62 - 18.28: 4 Bond angle restraints: 14118 Sorted by residual: angle pdb=" C23 9IM A 402 " pdb=" C30 9IM A 402 " pdb=" F31 9IM A 402 " ideal model delta sigma weight residual 118.60 136.88 -18.28 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C23 9IM C 402 " pdb=" C30 9IM C 402 " pdb=" F31 9IM C 402 " ideal model delta sigma weight residual 118.60 136.83 -18.23 3.00e+00 1.11e-01 3.69e+01 angle pdb=" C08 9IM C 402 " pdb=" C09 9IM C 402 " pdb=" F10 9IM C 402 " ideal model delta sigma weight residual 118.31 133.27 -14.96 3.00e+00 1.11e-01 2.49e+01 angle pdb=" C08 9IM A 402 " pdb=" C09 9IM A 402 " pdb=" F10 9IM A 402 " ideal model delta sigma weight residual 118.31 133.03 -14.72 3.00e+00 1.11e-01 2.41e+01 angle pdb=" C08 9IM A 402 " pdb=" C14 9IM A 402 " pdb="CL1 9IM A 402 " ideal model delta sigma weight residual 119.61 134.07 -14.46 3.00e+00 1.11e-01 2.32e+01 ... (remaining 14113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 5406 17.20 - 34.39: 611 34.39 - 51.58: 99 51.58 - 68.78: 14 68.78 - 85.97: 12 Dihedral angle restraints: 6142 sinusoidal: 2470 harmonic: 3672 Sorted by residual: dihedral pdb=" CA ILE D 171 " pdb=" C ILE D 171 " pdb=" N LEU D 172 " pdb=" CA LEU D 172 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA GLU B 38 " pdb=" C GLU B 38 " pdb=" N PRO B 39 " pdb=" CA PRO B 39 " ideal model delta harmonic sigma weight residual 180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA GLU D 38 " pdb=" C GLU D 38 " pdb=" N PRO D 39 " pdb=" CA PRO D 39 " ideal model delta harmonic sigma weight residual 180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 6139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1039 0.030 - 0.061: 350 0.061 - 0.091: 93 0.091 - 0.122: 67 0.122 - 0.152: 9 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CA ILE A 219 " pdb=" N ILE A 219 " pdb=" C ILE A 219 " pdb=" CB ILE A 219 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA ILE A 312 " pdb=" N ILE A 312 " pdb=" C ILE A 312 " pdb=" CB ILE A 312 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE D 219 " pdb=" N ILE D 219 " pdb=" C ILE D 219 " pdb=" CB ILE D 219 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 1555 not shown) Planarity restraints: 1798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 106 " 0.016 2.00e-02 2.50e+03 1.11e-02 2.46e+00 pdb=" CG TYR D 106 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR D 106 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR D 106 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 106 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 106 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR D 106 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 106 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 263 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 264 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 264 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 264 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 140 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO C 141 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 141 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 141 " -0.020 5.00e-02 4.00e+02 ... (remaining 1795 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1019 2.75 - 3.29: 9855 3.29 - 3.82: 17367 3.82 - 4.36: 20350 4.36 - 4.90: 35664 Nonbonded interactions: 84255 Sorted by model distance: nonbonded pdb=" O GLY A 234 " pdb=" OH TYR B 245 " model vdw 2.209 3.040 nonbonded pdb=" NH2 ARG B 45 " pdb=" O PRO B 110 " model vdw 2.219 3.120 nonbonded pdb=" NH2 ARG D 45 " pdb=" O PRO D 110 " model vdw 2.257 3.120 nonbonded pdb=" NH1 ARG A 45 " pdb=" OE2 GLU C 41 " model vdw 2.304 3.120 nonbonded pdb=" OH TYR A 167 " pdb=" OE1 GLU A 260 " model vdw 2.307 3.040 ... (remaining 84250 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 110 or resid 116 through 333 or resid 401)) selection = chain 'B' selection = (chain 'C' and (resid 5 through 110 or resid 116 through 333 or resid 401)) selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 1.790 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.230 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.006 0.135 10380 Z= 0.284 Angle : 0.758 18.277 14118 Z= 0.324 Chirality : 0.039 0.152 1558 Planarity : 0.004 0.038 1798 Dihedral : 14.488 85.974 3790 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 2.20 (0.25), residues: 1238 helix: 2.47 (0.18), residues: 746 sheet: -1.01 (0.39), residues: 154 loop : 0.49 (0.39), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 119 HIS 0.003 0.001 HIS A 232 PHE 0.012 0.001 PHE B 279 TYR 0.027 0.001 TYR D 106 ARG 0.002 0.000 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.10921 ( 643) hydrogen bonds : angle 6.18947 ( 1890) covalent geometry : bond 0.00582 (10380) covalent geometry : angle 0.75811 (14118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7057 (ttm110) cc_final: 0.6201 (mtt90) REVERT: A 106 TYR cc_start: 0.7523 (t80) cc_final: 0.7130 (t80) REVERT: A 197 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7303 (mtp85) REVERT: A 218 ASN cc_start: 0.8049 (m-40) cc_final: 0.7758 (m-40) REVERT: B 120 MET cc_start: 0.7430 (mmt) cc_final: 0.6804 (mmt) REVERT: B 180 ARG cc_start: 0.6448 (ttp-110) cc_final: 0.6187 (mtp-110) REVERT: B 326 SER cc_start: 0.7507 (p) cc_final: 0.7293 (p) REVERT: C 218 ASN cc_start: 0.8047 (m-40) cc_final: 0.7739 (m-40) REVERT: D 120 MET cc_start: 0.7630 (mmt) cc_final: 0.7131 (mmt) REVERT: D 220 ARG cc_start: 0.6674 (mtm110) cc_final: 0.6226 (mtp-110) REVERT: D 310 ARG cc_start: 0.7979 (tpt170) cc_final: 0.7702 (tpt90) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3423 time to fit residues: 53.0993 Evaluate side-chains 115 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 HIS B 332 HIS D 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.148775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.121080 restraints weight = 11033.033| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.74 r_work: 0.3208 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10380 Z= 0.175 Angle : 0.559 6.551 14118 Z= 0.279 Chirality : 0.040 0.151 1558 Planarity : 0.004 0.038 1798 Dihedral : 4.427 29.225 1450 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.56 % Allowed : 5.25 % Favored : 94.18 % 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: 2.05 (0.25), residues: 1238 helix: 2.38 (0.18), residues: 748 sheet: -0.78 (0.40), residues: 142 loop : 0.12 (0.39), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.004 0.001 HIS B 332 PHE 0.012 0.002 PHE B 279 TYR 0.019 0.001 TYR C 106 ARG 0.002 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 643) hydrogen bonds : angle 4.89238 ( 1890) covalent geometry : bond 0.00418 (10380) covalent geometry : angle 0.55936 (14118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 1.148 Fit side-chains REVERT: A 106 TYR cc_start: 0.7688 (t80) cc_final: 0.7270 (t80) REVERT: A 176 GLN cc_start: 0.7461 (mm-40) cc_final: 0.7207 (mm-40) REVERT: A 218 ASN cc_start: 0.8051 (m-40) cc_final: 0.7767 (m-40) REVERT: B 180 ARG cc_start: 0.6529 (ttp-110) cc_final: 0.6188 (mtp-110) REVERT: B 214 MET cc_start: 0.7825 (mmt) cc_final: 0.7134 (ttt) REVERT: B 245 TYR cc_start: 0.8745 (m-80) cc_final: 0.8351 (m-80) REVERT: B 324 SER cc_start: 0.7997 (p) cc_final: 0.7796 (p) REVERT: C 218 ASN cc_start: 0.7977 (m-40) cc_final: 0.7672 (m-40) REVERT: D 120 MET cc_start: 0.7695 (mmt) cc_final: 0.7001 (mmm) REVERT: D 220 ARG cc_start: 0.6675 (mtm110) cc_final: 0.6207 (mtp-110) REVERT: D 310 ARG cc_start: 0.8033 (tpt170) cc_final: 0.7762 (tpt90) outliers start: 6 outliers final: 5 residues processed: 128 average time/residue: 0.3098 time to fit residues: 51.2304 Evaluate side-chains 125 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 256 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 56 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.151441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.123910 restraints weight = 11147.045| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.75 r_work: 0.3195 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10380 Z= 0.132 Angle : 0.495 5.135 14118 Z= 0.251 Chirality : 0.038 0.141 1558 Planarity : 0.004 0.038 1798 Dihedral : 4.194 26.075 1450 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.94 % Allowed : 7.50 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.26 (0.25), residues: 1238 helix: 2.56 (0.18), residues: 748 sheet: -0.65 (0.41), residues: 142 loop : 0.13 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 161 HIS 0.003 0.001 HIS A 232 PHE 0.010 0.001 PHE B 279 TYR 0.019 0.001 TYR C 106 ARG 0.001 0.000 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 643) hydrogen bonds : angle 4.59021 ( 1890) covalent geometry : bond 0.00306 (10380) covalent geometry : angle 0.49497 (14118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 1.046 Fit side-chains REVERT: A 106 TYR cc_start: 0.7628 (t80) cc_final: 0.7186 (t80) REVERT: A 120 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.8029 (tmm) REVERT: A 218 ASN cc_start: 0.7975 (m-40) cc_final: 0.7705 (m-40) REVERT: A 220 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.6985 (ptm160) REVERT: B 120 MET cc_start: 0.7387 (mmt) cc_final: 0.6745 (mmt) REVERT: B 180 ARG cc_start: 0.6538 (ttp-110) cc_final: 0.5979 (mtm-85) REVERT: B 214 MET cc_start: 0.7746 (mmt) cc_final: 0.7089 (ttt) REVERT: B 246 GLU cc_start: 0.7282 (tp30) cc_final: 0.6988 (tp30) REVERT: C 120 MET cc_start: 0.8233 (ttp) cc_final: 0.8031 (ttp) REVERT: C 218 ASN cc_start: 0.7979 (m-40) cc_final: 0.7686 (m-40) REVERT: D 120 MET cc_start: 0.7616 (mmt) cc_final: 0.7163 (mmt) REVERT: D 214 MET cc_start: 0.7814 (mmt) cc_final: 0.7138 (ttt) REVERT: D 220 ARG cc_start: 0.6616 (mtm110) cc_final: 0.6139 (mtp-110) REVERT: D 310 ARG cc_start: 0.8028 (tpt170) cc_final: 0.7760 (tpt90) outliers start: 10 outliers final: 6 residues processed: 131 average time/residue: 0.3142 time to fit residues: 53.6082 Evaluate side-chains 126 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.0060 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.147677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.120163 restraints weight = 11159.636| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.73 r_work: 0.3148 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10380 Z= 0.164 Angle : 0.524 5.354 14118 Z= 0.265 Chirality : 0.039 0.144 1558 Planarity : 0.004 0.038 1798 Dihedral : 4.250 26.793 1450 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.22 % Allowed : 9.76 % Favored : 89.02 % 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: 2.11 (0.25), residues: 1238 helix: 2.44 (0.18), residues: 748 sheet: -0.62 (0.41), residues: 142 loop : 0.01 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.003 0.001 HIS A 157 PHE 0.010 0.002 PHE A 291 TYR 0.019 0.001 TYR C 106 ARG 0.002 0.000 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 643) hydrogen bonds : angle 4.63363 ( 1890) covalent geometry : bond 0.00392 (10380) covalent geometry : angle 0.52440 (14118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.020 Fit side-chains REVERT: A 106 TYR cc_start: 0.7681 (t80) cc_final: 0.7425 (t80) REVERT: A 218 ASN cc_start: 0.8053 (m-40) cc_final: 0.7532 (m-40) REVERT: A 220 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.6838 (ptm160) REVERT: A 252 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6979 (mm-40) REVERT: A 271 MET cc_start: 0.8881 (mtm) cc_final: 0.8577 (mtp) REVERT: B 120 MET cc_start: 0.7384 (mmt) cc_final: 0.6773 (mmt) REVERT: B 180 ARG cc_start: 0.6601 (ttp-110) cc_final: 0.5993 (mtm-85) REVERT: B 214 MET cc_start: 0.7741 (mmt) cc_final: 0.7082 (ttt) REVERT: B 245 TYR cc_start: 0.8767 (m-80) cc_final: 0.8404 (m-80) REVERT: C 218 ASN cc_start: 0.7968 (m-40) cc_final: 0.7648 (m-40) REVERT: C 271 MET cc_start: 0.8900 (mtm) cc_final: 0.8563 (mtp) REVERT: D 120 MET cc_start: 0.7615 (mmt) cc_final: 0.6919 (mmm) REVERT: D 214 MET cc_start: 0.7858 (mmt) cc_final: 0.7284 (ttt) REVERT: D 220 ARG cc_start: 0.6671 (mtm110) cc_final: 0.6182 (mtp-110) REVERT: D 310 ARG cc_start: 0.8054 (tpt170) cc_final: 0.7773 (tpt90) outliers start: 13 outliers final: 8 residues processed: 128 average time/residue: 0.3150 time to fit residues: 51.9486 Evaluate side-chains 127 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 326 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.144922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.117409 restraints weight = 11227.394| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.74 r_work: 0.3085 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10380 Z= 0.214 Angle : 0.572 5.973 14118 Z= 0.287 Chirality : 0.041 0.149 1558 Planarity : 0.005 0.041 1798 Dihedral : 4.438 28.282 1450 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.41 % Allowed : 12.10 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.82 (0.25), residues: 1238 helix: 2.21 (0.18), residues: 748 sheet: -0.60 (0.41), residues: 142 loop : -0.17 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 161 HIS 0.004 0.001 HIS D 332 PHE 0.012 0.002 PHE A 291 TYR 0.024 0.001 TYR C 106 ARG 0.002 0.000 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 643) hydrogen bonds : angle 4.79117 ( 1890) covalent geometry : bond 0.00518 (10380) covalent geometry : angle 0.57197 (14118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.166 Fit side-chains REVERT: A 176 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7234 (mm-40) REVERT: A 218 ASN cc_start: 0.8029 (m-40) cc_final: 0.7727 (m-40) REVERT: A 220 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.6901 (ptm160) REVERT: A 252 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6992 (mm-40) REVERT: B 180 ARG cc_start: 0.6754 (ttp-110) cc_final: 0.6293 (mtm-85) REVERT: B 214 MET cc_start: 0.7830 (mmt) cc_final: 0.7198 (ttt) REVERT: B 246 GLU cc_start: 0.7397 (tp30) cc_final: 0.7044 (mm-30) REVERT: C 218 ASN cc_start: 0.8052 (m-40) cc_final: 0.7718 (m-40) REVERT: C 252 GLN cc_start: 0.7195 (mm110) cc_final: 0.6934 (mm-40) REVERT: D 120 MET cc_start: 0.7642 (mmt) cc_final: 0.6975 (mmm) REVERT: D 214 MET cc_start: 0.7906 (mmt) cc_final: 0.7337 (ttt) REVERT: D 220 ARG cc_start: 0.6771 (mtm110) cc_final: 0.6264 (mtp-110) REVERT: D 310 ARG cc_start: 0.8107 (tpt170) cc_final: 0.7836 (tpt90) outliers start: 15 outliers final: 9 residues processed: 130 average time/residue: 0.3073 time to fit residues: 52.3203 Evaluate side-chains 132 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 326 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.149343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.122102 restraints weight = 11115.261| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.72 r_work: 0.3171 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10380 Z= 0.128 Angle : 0.484 5.245 14118 Z= 0.247 Chirality : 0.038 0.144 1558 Planarity : 0.004 0.039 1798 Dihedral : 4.156 25.649 1450 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.59 % Allowed : 12.20 % Favored : 86.21 % 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: 2.17 (0.25), residues: 1238 helix: 2.53 (0.18), residues: 750 sheet: -0.60 (0.41), residues: 142 loop : -0.05 (0.38), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.003 0.001 HIS A 232 PHE 0.008 0.001 PHE B 279 TYR 0.022 0.001 TYR C 106 ARG 0.001 0.000 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 643) hydrogen bonds : angle 4.44749 ( 1890) covalent geometry : bond 0.00299 (10380) covalent geometry : angle 0.48429 (14118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.182 Fit side-chains REVERT: A 106 TYR cc_start: 0.7674 (t80) cc_final: 0.7315 (t80) REVERT: A 218 ASN cc_start: 0.8050 (m-40) cc_final: 0.7773 (m-40) REVERT: A 220 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7374 (ptm160) REVERT: A 252 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6990 (mm-40) REVERT: B 33 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7167 (mp) REVERT: B 120 MET cc_start: 0.7423 (mmt) cc_final: 0.6786 (mmt) REVERT: B 180 ARG cc_start: 0.6647 (ttp-110) cc_final: 0.6203 (mtm-85) REVERT: B 214 MET cc_start: 0.7731 (mmt) cc_final: 0.7087 (ttt) REVERT: B 246 GLU cc_start: 0.7353 (tp30) cc_final: 0.6938 (mm-30) REVERT: C 218 ASN cc_start: 0.7974 (m-40) cc_final: 0.7651 (m-40) REVERT: C 252 GLN cc_start: 0.7198 (mm110) cc_final: 0.6935 (mm-40) REVERT: C 301 ASP cc_start: 0.7117 (t0) cc_final: 0.6839 (t0) REVERT: D 120 MET cc_start: 0.7569 (mmt) cc_final: 0.7060 (mmt) REVERT: D 214 MET cc_start: 0.7807 (mmt) cc_final: 0.7336 (ttt) REVERT: D 220 ARG cc_start: 0.6689 (mtm110) cc_final: 0.6189 (mtp-110) REVERT: D 310 ARG cc_start: 0.8073 (tpt170) cc_final: 0.7789 (tpt90) outliers start: 17 outliers final: 6 residues processed: 136 average time/residue: 0.3104 time to fit residues: 54.9441 Evaluate side-chains 132 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 237 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.147032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.120003 restraints weight = 11240.279| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.70 r_work: 0.3196 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10380 Z= 0.159 Angle : 0.514 5.550 14118 Z= 0.262 Chirality : 0.039 0.146 1558 Planarity : 0.004 0.043 1798 Dihedral : 4.244 26.875 1450 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.41 % Allowed : 13.13 % Favored : 85.46 % 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: 2.08 (0.25), residues: 1238 helix: 2.48 (0.18), residues: 750 sheet: -0.61 (0.41), residues: 142 loop : -0.17 (0.38), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.004 0.001 HIS D 332 PHE 0.010 0.002 PHE A 117 TYR 0.021 0.001 TYR C 106 ARG 0.003 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 643) hydrogen bonds : angle 4.52341 ( 1890) covalent geometry : bond 0.00377 (10380) covalent geometry : angle 0.51446 (14118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.161 Fit side-chains REVERT: A 106 TYR cc_start: 0.7657 (t80) cc_final: 0.7439 (t80) REVERT: A 176 GLN cc_start: 0.7340 (mm-40) cc_final: 0.7093 (mm-40) REVERT: A 218 ASN cc_start: 0.8046 (m-40) cc_final: 0.7765 (m-40) REVERT: A 220 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7456 (ptm160) REVERT: A 252 GLN cc_start: 0.7256 (mm-40) cc_final: 0.7030 (mm-40) REVERT: A 271 MET cc_start: 0.8875 (mtm) cc_final: 0.8537 (mtp) REVERT: B 33 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7273 (mp) REVERT: B 120 MET cc_start: 0.7458 (mmt) cc_final: 0.6804 (mmt) REVERT: B 180 ARG cc_start: 0.6672 (ttp-110) cc_final: 0.6208 (mtm-85) REVERT: B 214 MET cc_start: 0.7756 (mmt) cc_final: 0.7180 (ttt) REVERT: B 246 GLU cc_start: 0.7406 (tp30) cc_final: 0.6941 (mm-30) REVERT: C 218 ASN cc_start: 0.8015 (m-40) cc_final: 0.7670 (m-40) REVERT: C 252 GLN cc_start: 0.7206 (mm110) cc_final: 0.6943 (mm-40) REVERT: C 271 MET cc_start: 0.8887 (mtm) cc_final: 0.8541 (mtp) REVERT: D 120 MET cc_start: 0.7539 (mmt) cc_final: 0.6819 (mmm) REVERT: D 214 MET cc_start: 0.7848 (mmt) cc_final: 0.7357 (ttt) REVERT: D 220 ARG cc_start: 0.6674 (mtm110) cc_final: 0.6142 (mtp-110) REVERT: D 310 ARG cc_start: 0.8042 (tpt170) cc_final: 0.7754 (tpt90) outliers start: 15 outliers final: 9 residues processed: 131 average time/residue: 0.3086 time to fit residues: 52.6280 Evaluate side-chains 131 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 237 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.145706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118548 restraints weight = 11339.113| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.71 r_work: 0.3138 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10380 Z= 0.174 Angle : 0.530 5.685 14118 Z= 0.269 Chirality : 0.039 0.145 1558 Planarity : 0.005 0.047 1798 Dihedral : 4.313 27.319 1450 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.41 % Allowed : 13.88 % Favored : 84.71 % 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: 2.00 (0.25), residues: 1238 helix: 2.39 (0.18), residues: 750 sheet: -0.55 (0.41), residues: 132 loop : -0.21 (0.38), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 119 HIS 0.003 0.001 HIS D 332 PHE 0.011 0.002 PHE A 117 TYR 0.022 0.001 TYR C 106 ARG 0.002 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 643) hydrogen bonds : angle 4.57944 ( 1890) covalent geometry : bond 0.00415 (10380) covalent geometry : angle 0.53000 (14118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.147 Fit side-chains REVERT: A 176 GLN cc_start: 0.7451 (mm-40) cc_final: 0.7202 (mm-40) REVERT: A 218 ASN cc_start: 0.7988 (m-40) cc_final: 0.7698 (m-40) REVERT: A 220 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7386 (ptm160) REVERT: B 33 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7356 (mp) REVERT: B 120 MET cc_start: 0.7451 (mmt) cc_final: 0.6622 (mmt) REVERT: B 180 ARG cc_start: 0.6727 (ttp-110) cc_final: 0.6179 (mtp-110) REVERT: B 214 MET cc_start: 0.7762 (mmt) cc_final: 0.7229 (ttt) REVERT: B 246 GLU cc_start: 0.7498 (tp30) cc_final: 0.6999 (mm-30) REVERT: C 218 ASN cc_start: 0.8020 (m-40) cc_final: 0.7681 (m-40) REVERT: C 252 GLN cc_start: 0.7248 (mm110) cc_final: 0.6984 (mm-40) REVERT: D 120 MET cc_start: 0.7602 (mmt) cc_final: 0.6887 (mmm) REVERT: D 214 MET cc_start: 0.7878 (mmt) cc_final: 0.7446 (ttt) REVERT: D 220 ARG cc_start: 0.6707 (mtm110) cc_final: 0.6177 (mtp-110) REVERT: D 310 ARG cc_start: 0.8076 (tpt170) cc_final: 0.7784 (tpt90) outliers start: 15 outliers final: 11 residues processed: 132 average time/residue: 0.2995 time to fit residues: 51.7648 Evaluate side-chains 137 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 237 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 7.9990 chunk 117 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.150166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.123250 restraints weight = 11249.260| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.71 r_work: 0.3231 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10380 Z= 0.121 Angle : 0.479 5.253 14118 Z= 0.245 Chirality : 0.037 0.139 1558 Planarity : 0.004 0.048 1798 Dihedral : 4.078 24.331 1450 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.31 % Allowed : 14.17 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.25), residues: 1238 helix: 2.64 (0.18), residues: 752 sheet: -0.44 (0.42), residues: 128 loop : -0.09 (0.38), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.004 0.001 HIS A 232 PHE 0.008 0.001 PHE B 279 TYR 0.019 0.001 TYR A 106 ARG 0.002 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 643) hydrogen bonds : angle 4.35382 ( 1890) covalent geometry : bond 0.00280 (10380) covalent geometry : angle 0.47917 (14118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.094 Fit side-chains REVERT: A 106 TYR cc_start: 0.7695 (t80) cc_final: 0.7360 (t80) REVERT: A 218 ASN cc_start: 0.8056 (m-40) cc_final: 0.7788 (m-40) REVERT: A 220 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7444 (ptm160) REVERT: B 33 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7075 (mp) REVERT: B 99 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6738 (tp) REVERT: B 120 MET cc_start: 0.7510 (mmt) cc_final: 0.6727 (mmt) REVERT: B 180 ARG cc_start: 0.6677 (ttp-110) cc_final: 0.6216 (mtm-85) REVERT: B 214 MET cc_start: 0.7723 (mmt) cc_final: 0.7173 (ttt) REVERT: B 246 GLU cc_start: 0.7429 (tp30) cc_final: 0.6951 (mm-30) REVERT: C 106 TYR cc_start: 0.7736 (t80) cc_final: 0.7368 (t80) REVERT: C 218 ASN cc_start: 0.7975 (m-40) cc_final: 0.7643 (m-40) REVERT: C 252 GLN cc_start: 0.7230 (mm110) cc_final: 0.6966 (mm-40) REVERT: D 120 MET cc_start: 0.7528 (mmt) cc_final: 0.6816 (mmm) REVERT: D 214 MET cc_start: 0.7842 (mmt) cc_final: 0.7503 (ttt) REVERT: D 220 ARG cc_start: 0.6635 (mtm110) cc_final: 0.6114 (mtp-110) REVERT: D 310 ARG cc_start: 0.8047 (tpt170) cc_final: 0.7758 (tpt90) outliers start: 14 outliers final: 10 residues processed: 139 average time/residue: 0.3001 time to fit residues: 54.6333 Evaluate side-chains 138 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 237 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.149963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.122862 restraints weight = 11180.396| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.72 r_work: 0.3161 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10380 Z= 0.125 Angle : 0.483 5.162 14118 Z= 0.246 Chirality : 0.038 0.142 1558 Planarity : 0.004 0.052 1798 Dihedral : 4.058 24.394 1450 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.31 % Allowed : 14.07 % Favored : 84.62 % 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: 2.34 (0.25), residues: 1238 helix: 2.68 (0.18), residues: 750 sheet: -0.48 (0.43), residues: 128 loop : -0.11 (0.38), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.003 0.001 HIS A 232 PHE 0.008 0.001 PHE B 221 TYR 0.020 0.001 TYR A 106 ARG 0.002 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 643) hydrogen bonds : angle 4.33426 ( 1890) covalent geometry : bond 0.00291 (10380) covalent geometry : angle 0.48306 (14118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.060 Fit side-chains REVERT: A 106 TYR cc_start: 0.7636 (t80) cc_final: 0.7355 (t80) REVERT: A 218 ASN cc_start: 0.8053 (m-40) cc_final: 0.7790 (m-40) REVERT: A 220 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7467 (ptm160) REVERT: B 33 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7171 (mp) REVERT: B 99 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6823 (tp) REVERT: B 120 MET cc_start: 0.7571 (mmt) cc_final: 0.6864 (mmt) REVERT: B 180 ARG cc_start: 0.6745 (ttp-110) cc_final: 0.6276 (mtm-85) REVERT: B 214 MET cc_start: 0.7715 (mmt) cc_final: 0.7199 (ttt) REVERT: B 218 ASN cc_start: 0.7962 (t0) cc_final: 0.7760 (t0) REVERT: B 246 GLU cc_start: 0.7490 (tp30) cc_final: 0.6990 (mm-30) REVERT: C 218 ASN cc_start: 0.7956 (m-40) cc_final: 0.7630 (m-40) REVERT: C 252 GLN cc_start: 0.7216 (mm110) cc_final: 0.6955 (mm-40) REVERT: D 120 MET cc_start: 0.7594 (mmt) cc_final: 0.6914 (mmm) REVERT: D 214 MET cc_start: 0.7783 (mmt) cc_final: 0.7445 (ttt) REVERT: D 220 ARG cc_start: 0.6665 (mtm110) cc_final: 0.6143 (mtp-110) REVERT: D 310 ARG cc_start: 0.8063 (tpt170) cc_final: 0.7775 (tpt90) outliers start: 14 outliers final: 10 residues processed: 135 average time/residue: 0.3190 time to fit residues: 57.1955 Evaluate side-chains 135 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 237 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 86 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.153811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127265 restraints weight = 11030.746| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.69 r_work: 0.3179 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10380 Z= 0.114 Angle : 0.469 5.100 14118 Z= 0.240 Chirality : 0.037 0.139 1558 Planarity : 0.004 0.051 1798 Dihedral : 3.953 23.328 1450 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.31 % Allowed : 14.17 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.25), residues: 1238 helix: 2.78 (0.18), residues: 750 sheet: -0.47 (0.43), residues: 128 loop : -0.04 (0.38), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.003 0.001 HIS A 232 PHE 0.008 0.001 PHE B 279 TYR 0.019 0.001 TYR A 106 ARG 0.002 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 643) hydrogen bonds : angle 4.24901 ( 1890) covalent geometry : bond 0.00261 (10380) covalent geometry : angle 0.46852 (14118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5242.41 seconds wall clock time: 91 minutes 39.59 seconds (5499.59 seconds total)