Starting phenix.real_space_refine on Wed Apr 30 23:19:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ct3_45897/04_2025/9ct3_45897.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ct3_45897/04_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_45897/04_2025/9ct3_45897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ct3_45897/04_2025/9ct3_45897.map" model { file = "/net/cci-nas-00/data/ceres_data/9ct3_45897/04_2025/9ct3_45897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ct3_45897/04_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 7.18, per 1000 atoms: 0.71 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: 2.90 Conformation dependent library (CDL) restraints added in 1.2 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: 1.01 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: 2.69 Time building geometry restraints manager: 3.33 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: 0.02 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: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.000 Find NCS groups from input model: 0.480 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.460 ------------------------------------------------------------------------------- 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 : 1.163 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: 0.3413 time to fit residues: 53.4028 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 : 1.228 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.121083 restraints weight = 11033.032| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.74 r_work: 0.3227 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 1.209 Fit side-chains REVERT: A 106 TYR cc_start: 0.7684 (t80) cc_final: 0.7265 (t80) REVERT: A 176 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7187 (mm-40) REVERT: A 218 ASN cc_start: 0.8046 (m-40) cc_final: 0.7761 (m-40) REVERT: B 180 ARG cc_start: 0.6495 (ttp-110) cc_final: 0.6155 (mtp-110) REVERT: B 214 MET cc_start: 0.7816 (mmt) cc_final: 0.7128 (ttt) REVERT: B 245 TYR cc_start: 0.8732 (m-80) cc_final: 0.8334 (m-80) REVERT: B 324 SER cc_start: 0.7991 (p) cc_final: 0.7787 (p) REVERT: C 218 ASN cc_start: 0.7970 (m-40) cc_final: 0.7666 (m-40) REVERT: D 120 MET cc_start: 0.7682 (mmt) cc_final: 0.6988 (mmm) REVERT: D 220 ARG cc_start: 0.6643 (mtm110) cc_final: 0.6174 (mtp-110) REVERT: D 310 ARG cc_start: 0.8026 (tpt170) cc_final: 0.7753 (tpt90) outliers start: 6 outliers final: 5 residues processed: 128 average time/residue: 0.3179 time to fit residues: 52.8469 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 : 0.978 ------------------------------------------------------------------------------- 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: 1.9990 chunk 88 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.147959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120370 restraints weight = 11193.157| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.74 r_work: 0.3190 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10380 Z= 0.180 Angle : 0.546 5.597 14118 Z= 0.275 Chirality : 0.040 0.146 1558 Planarity : 0.004 0.039 1798 Dihedral : 4.358 27.382 1450 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.03 % Allowed : 7.69 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.25), residues: 1238 helix: 2.31 (0.18), residues: 748 sheet: -0.69 (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 0.011 0.002 PHE A 291 TYR 0.022 0.001 TYR C 106 ARG 0.002 0.000 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 643) hydrogen bonds : angle 4.78835 ( 1890) covalent geometry : bond 0.00433 (10380) covalent geometry : angle 0.54569 (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 137 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.992 Fit side-chains REVERT: A 106 TYR cc_start: 0.7686 (t80) cc_final: 0.7449 (t80) REVERT: A 218 ASN cc_start: 0.8058 (m-40) cc_final: 0.7773 (m-40) REVERT: A 220 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7028 (ptm160) REVERT: A 252 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6995 (mm-40) REVERT: A 271 MET cc_start: 0.8885 (mtm) cc_final: 0.8561 (mtp) REVERT: B 180 ARG cc_start: 0.6600 (ttp-110) cc_final: 0.5999 (mtm-85) REVERT: B 214 MET cc_start: 0.7790 (mmt) cc_final: 0.7060 (ttt) REVERT: B 245 TYR cc_start: 0.8806 (m-80) cc_final: 0.8477 (m-80) REVERT: C 120 MET cc_start: 0.8318 (ttp) cc_final: 0.8087 (ttp) REVERT: C 218 ASN cc_start: 0.8008 (m-40) cc_final: 0.7696 (m-40) REVERT: D 120 MET cc_start: 0.7634 (mmt) cc_final: 0.6926 (mmm) REVERT: D 214 MET cc_start: 0.7874 (mmt) cc_final: 0.7218 (ttt) REVERT: D 220 ARG cc_start: 0.6654 (mtm110) cc_final: 0.6169 (mtp-110) REVERT: D 310 ARG cc_start: 0.8043 (tpt170) cc_final: 0.7767 (tpt90) outliers start: 11 outliers final: 5 residues processed: 131 average time/residue: 0.3126 time to fit residues: 52.9071 Evaluate side-chains 126 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 326 SER Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 237 ASP 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: 5.9990 chunk 27 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.0040 chunk 12 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.152913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125779 restraints weight = 11085.520| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.73 r_work: 0.3200 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10380 Z= 0.110 Angle : 0.471 5.124 14118 Z= 0.240 Chirality : 0.037 0.139 1558 Planarity : 0.004 0.038 1798 Dihedral : 4.030 23.324 1450 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.03 % Allowed : 9.94 % 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: 2.39 (0.25), residues: 1238 helix: 2.68 (0.18), residues: 748 sheet: -0.56 (0.42), residues: 138 loop : 0.11 (0.38), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.003 0.000 HIS A 232 PHE 0.008 0.001 PHE B 279 TYR 0.018 0.001 TYR C 106 ARG 0.001 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 643) hydrogen bonds : angle 4.38618 ( 1890) covalent geometry : bond 0.00248 (10380) covalent geometry : angle 0.47054 (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 138 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.204 Fit side-chains REVERT: A 106 TYR cc_start: 0.7654 (t80) cc_final: 0.7196 (t80) REVERT: A 120 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7987 (tmm) REVERT: A 218 ASN cc_start: 0.7971 (m-40) cc_final: 0.7718 (m-40) REVERT: A 220 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7394 (ptm160) REVERT: A 252 GLN cc_start: 0.7164 (mm-40) cc_final: 0.6942 (mm-40) REVERT: B 120 MET cc_start: 0.7449 (mmt) cc_final: 0.6830 (mmt) REVERT: B 180 ARG cc_start: 0.6556 (ttp-110) cc_final: 0.5992 (mtm-85) REVERT: B 214 MET cc_start: 0.7696 (mmt) cc_final: 0.7075 (ttt) REVERT: B 245 TYR cc_start: 0.8796 (m-80) cc_final: 0.8478 (m-80) REVERT: B 246 GLU cc_start: 0.7236 (tp30) cc_final: 0.6847 (tp30) REVERT: C 218 ASN cc_start: 0.7978 (m-40) cc_final: 0.7688 (m-40) REVERT: D 120 MET cc_start: 0.7587 (mmt) cc_final: 0.7158 (mmt) REVERT: D 214 MET cc_start: 0.7780 (mmt) cc_final: 0.7227 (ttt) REVERT: D 220 ARG cc_start: 0.6645 (mtm110) cc_final: 0.6154 (mtp-110) REVERT: D 310 ARG cc_start: 0.8030 (tpt170) cc_final: 0.7751 (tpt90) outliers start: 11 outliers final: 5 residues processed: 130 average time/residue: 0.3566 time to fit residues: 60.2374 Evaluate side-chains 127 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain C residue 80 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: 5.9990 chunk 73 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.148396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120990 restraints weight = 11157.115| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.73 r_work: 0.3202 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10380 Z= 0.188 Angle : 0.539 5.695 14118 Z= 0.272 Chirality : 0.040 0.145 1558 Planarity : 0.005 0.039 1798 Dihedral : 4.290 27.368 1450 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.50 % Allowed : 11.73 % Favored : 86.77 % 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: 2.41 (0.18), residues: 748 sheet: -0.58 (0.41), residues: 142 loop : -0.06 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.003 0.001 HIS A 157 PHE 0.012 0.002 PHE A 117 TYR 0.021 0.001 TYR C 106 ARG 0.002 0.000 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 643) hydrogen bonds : angle 4.63646 ( 1890) covalent geometry : bond 0.00452 (10380) covalent geometry : angle 0.53892 (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 132 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 2.106 Fit side-chains REVERT: A 218 ASN cc_start: 0.8051 (m-40) cc_final: 0.7763 (m-40) REVERT: A 220 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.6914 (ptm160) REVERT: A 252 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6975 (mm-40) REVERT: A 271 MET cc_start: 0.8905 (mtm) cc_final: 0.8576 (mtp) REVERT: B 120 MET cc_start: 0.7432 (mmt) cc_final: 0.6829 (mmt) REVERT: B 180 ARG cc_start: 0.6649 (ttp-110) cc_final: 0.6022 (mtm-85) REVERT: B 214 MET cc_start: 0.7783 (mmt) cc_final: 0.7117 (ttt) REVERT: C 218 ASN cc_start: 0.8001 (m-40) cc_final: 0.7677 (m-40) REVERT: C 252 GLN cc_start: 0.7198 (mm110) cc_final: 0.6927 (mm-40) REVERT: D 120 MET cc_start: 0.7622 (mmt) cc_final: 0.6906 (mmm) REVERT: D 214 MET cc_start: 0.7913 (mmt) cc_final: 0.7271 (ttt) REVERT: D 220 ARG cc_start: 0.6729 (mtm110) cc_final: 0.6226 (mtp-110) REVERT: D 310 ARG cc_start: 0.8033 (tpt170) cc_final: 0.7754 (tpt90) outliers start: 16 outliers final: 7 residues processed: 126 average time/residue: 0.3785 time to fit residues: 62.5860 Evaluate side-chains 124 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 256 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.151755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124715 restraints weight = 11079.443| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.72 r_work: 0.3232 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1371 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= 0.121 Angle : 0.478 5.176 14118 Z= 0.244 Chirality : 0.038 0.143 1558 Planarity : 0.004 0.041 1798 Dihedral : 4.079 24.825 1450 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.41 % Allowed : 12.57 % Favored : 86.02 % 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: 2.32 (0.25), residues: 1238 helix: 2.65 (0.18), residues: 748 sheet: -0.58 (0.41), residues: 142 loop : 0.02 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 119 HIS 0.003 0.000 HIS A 232 PHE 0.008 0.001 PHE B 279 TYR 0.019 0.001 TYR C 106 ARG 0.001 0.000 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 643) hydrogen bonds : angle 4.37661 ( 1890) covalent geometry : bond 0.00279 (10380) covalent geometry : angle 0.47763 (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 134 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.015 Fit side-chains REVERT: A 106 TYR cc_start: 0.7689 (t80) cc_final: 0.7390 (t80) REVERT: A 218 ASN cc_start: 0.8032 (m-40) cc_final: 0.7776 (m-40) REVERT: A 220 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7429 (ptm160) REVERT: A 252 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6966 (mm-40) REVERT: B 120 MET cc_start: 0.7476 (mmt) cc_final: 0.6827 (mmt) REVERT: B 180 ARG cc_start: 0.6631 (ttp-110) cc_final: 0.6190 (mtm-85) REVERT: B 214 MET cc_start: 0.7724 (mmt) cc_final: 0.7186 (ttt) REVERT: B 246 GLU cc_start: 0.7328 (tp30) cc_final: 0.6921 (mm-30) REVERT: C 218 ASN cc_start: 0.7984 (m-40) cc_final: 0.7667 (m-40) REVERT: C 252 GLN cc_start: 0.7165 (mm110) cc_final: 0.6883 (mm-40) REVERT: D 107 TYR cc_start: 0.7691 (t80) cc_final: 0.7368 (t80) REVERT: D 120 MET cc_start: 0.7513 (mmt) cc_final: 0.6988 (mmt) REVERT: D 214 MET cc_start: 0.7798 (mmt) cc_final: 0.7316 (ttt) REVERT: D 220 ARG cc_start: 0.6676 (mtm110) cc_final: 0.6160 (mtp-110) REVERT: D 310 ARG cc_start: 0.8023 (tpt170) cc_final: 0.7733 (tpt90) outliers start: 15 outliers final: 8 residues processed: 128 average time/residue: 0.3165 time to fit residues: 52.8145 Evaluate side-chains 124 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.152888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.126204 restraints weight = 11070.909| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.69 r_work: 0.3241 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10380 Z= 0.154 Angle : 0.508 5.336 14118 Z= 0.258 Chirality : 0.039 0.146 1558 Planarity : 0.004 0.044 1798 Dihedral : 4.222 27.241 1450 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.78 % Allowed : 12.29 % Favored : 85.93 % 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: 2.21 (0.25), residues: 1238 helix: 2.55 (0.18), residues: 748 sheet: -0.56 (0.41), residues: 142 loop : -0.03 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.003 0.001 HIS A 232 PHE 0.010 0.002 PHE A 117 TYR 0.020 0.001 TYR C 106 ARG 0.002 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 643) hydrogen bonds : angle 4.47114 ( 1890) covalent geometry : bond 0.00365 (10380) covalent geometry : angle 0.50830 (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: 19 poor density : 117 time to evaluate : 0.968 Fit side-chains REVERT: A 106 TYR cc_start: 0.7678 (t80) cc_final: 0.7431 (t80) REVERT: A 218 ASN cc_start: 0.8012 (m-40) cc_final: 0.7748 (m-40) REVERT: A 220 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7382 (ptm160) REVERT: A 252 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6992 (mm-40) REVERT: A 271 MET cc_start: 0.8894 (mtm) cc_final: 0.8559 (mtp) REVERT: B 33 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7208 (mp) REVERT: B 120 MET cc_start: 0.7486 (mmt) cc_final: 0.6830 (mmt) REVERT: B 180 ARG cc_start: 0.6690 (ttp-110) cc_final: 0.6230 (mtm-85) REVERT: B 214 MET cc_start: 0.7780 (mmt) cc_final: 0.7214 (ttt) REVERT: B 246 GLU cc_start: 0.7445 (tp30) cc_final: 0.6996 (mm-30) REVERT: C 218 ASN cc_start: 0.7979 (m-40) cc_final: 0.7651 (m-40) REVERT: C 252 GLN cc_start: 0.7170 (mm110) cc_final: 0.6901 (mm-40) REVERT: D 107 TYR cc_start: 0.7941 (t80) cc_final: 0.7598 (t80) REVERT: D 120 MET cc_start: 0.7537 (mmt) cc_final: 0.6817 (mmm) REVERT: D 214 MET cc_start: 0.7850 (mmt) cc_final: 0.7350 (ttt) REVERT: D 220 ARG cc_start: 0.6719 (mtm110) cc_final: 0.6198 (mtp-110) REVERT: D 310 ARG cc_start: 0.8043 (tpt170) cc_final: 0.7757 (tpt90) outliers start: 19 outliers final: 9 residues processed: 130 average time/residue: 0.2992 time to fit residues: 50.8260 Evaluate side-chains 128 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.144124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.116919 restraints weight = 11397.118| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.71 r_work: 0.3109 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1645 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= 0.211 Angle : 0.567 5.947 14118 Z= 0.285 Chirality : 0.041 0.147 1558 Planarity : 0.005 0.047 1798 Dihedral : 4.445 28.887 1450 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.13 % Allowed : 13.60 % Favored : 85.27 % 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: 1.89 (0.24), residues: 1238 helix: 2.26 (0.18), residues: 750 sheet: -0.52 (0.41), residues: 132 loop : -0.18 (0.38), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 119 HIS 0.003 0.001 HIS A 157 PHE 0.013 0.002 PHE A 291 TYR 0.023 0.001 TYR C 106 ARG 0.002 0.000 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 643) hydrogen bonds : angle 4.69443 ( 1890) covalent geometry : bond 0.00510 (10380) covalent geometry : angle 0.56657 (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: 12 poor density : 126 time to evaluate : 1.175 Fit side-chains REVERT: A 218 ASN cc_start: 0.8026 (m-40) cc_final: 0.7718 (m-40) REVERT: A 220 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7005 (ptm160) REVERT: B 33 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7330 (mp) REVERT: B 120 MET cc_start: 0.7389 (mmt) cc_final: 0.6791 (mmt) REVERT: B 180 ARG cc_start: 0.6725 (ttp-110) cc_final: 0.6252 (mtm-85) REVERT: B 214 MET cc_start: 0.7756 (mmt) cc_final: 0.7234 (ttt) REVERT: B 246 GLU cc_start: 0.7447 (tp30) cc_final: 0.6975 (mm-30) REVERT: C 106 TYR cc_start: 0.7766 (t80) cc_final: 0.7424 (t80) REVERT: C 218 ASN cc_start: 0.8052 (m-40) cc_final: 0.7696 (m-40) REVERT: C 252 GLN cc_start: 0.7158 (mm110) cc_final: 0.6894 (mm-40) REVERT: C 301 ASP cc_start: 0.7189 (t0) cc_final: 0.6885 (t0) REVERT: D 120 MET cc_start: 0.7512 (mmt) cc_final: 0.6722 (mmm) REVERT: D 214 MET cc_start: 0.7819 (mmt) cc_final: 0.7395 (ttt) REVERT: D 220 ARG cc_start: 0.6680 (mtm110) cc_final: 0.6150 (mtp-110) REVERT: D 310 ARG cc_start: 0.8042 (tpt170) cc_final: 0.7755 (tpt90) outliers start: 12 outliers final: 8 residues processed: 135 average time/residue: 0.3244 time to fit residues: 57.9865 Evaluate side-chains 134 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.149075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.122054 restraints weight = 11251.094| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.70 r_work: 0.3146 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10380 Z= 0.143 Angle : 0.499 5.390 14118 Z= 0.256 Chirality : 0.038 0.142 1558 Planarity : 0.004 0.048 1798 Dihedral : 4.210 25.774 1450 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.94 % Allowed : 14.07 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.25), residues: 1238 helix: 2.48 (0.18), residues: 752 sheet: -0.52 (0.41), residues: 132 loop : -0.10 (0.38), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.004 0.001 HIS D 332 PHE 0.011 0.001 PHE D 117 TYR 0.022 0.001 TYR A 106 ARG 0.002 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 643) hydrogen bonds : angle 4.46320 ( 1890) covalent geometry : bond 0.00336 (10380) covalent geometry : angle 0.49931 (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 136 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 1.283 Fit side-chains REVERT: A 106 TYR cc_start: 0.7685 (t80) cc_final: 0.7390 (t80) REVERT: A 218 ASN cc_start: 0.8011 (m-40) cc_final: 0.7734 (m-40) REVERT: A 220 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7339 (ptm160) REVERT: B 120 MET cc_start: 0.7506 (mmt) cc_final: 0.6850 (mmt) REVERT: B 180 ARG cc_start: 0.6794 (ttp-110) cc_final: 0.6336 (mtm-85) REVERT: B 214 MET cc_start: 0.7753 (mmt) cc_final: 0.7187 (ttt) REVERT: B 246 GLU cc_start: 0.7483 (tp30) cc_final: 0.7020 (mm-30) REVERT: C 218 ASN cc_start: 0.8038 (m-40) cc_final: 0.7700 (m-40) REVERT: C 252 GLN cc_start: 0.7189 (mm110) cc_final: 0.6924 (mm-40) REVERT: D 120 MET cc_start: 0.7448 (mmt) cc_final: 0.6611 (mmt) REVERT: D 214 MET cc_start: 0.7876 (mmt) cc_final: 0.7498 (ttt) REVERT: D 220 ARG cc_start: 0.6758 (mtm110) cc_final: 0.6235 (mtp-110) REVERT: D 310 ARG cc_start: 0.8084 (tpt170) cc_final: 0.7804 (tpt90) outliers start: 10 outliers final: 8 residues processed: 133 average time/residue: 0.4106 time to fit residues: 71.3461 Evaluate side-chains 133 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 301 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.150476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123154 restraints weight = 11164.984| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.73 r_work: 0.3251 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 0.042 10380 Z= 0.122 Angle : 0.480 5.242 14118 Z= 0.246 Chirality : 0.037 0.141 1558 Planarity : 0.004 0.048 1798 Dihedral : 4.066 24.245 1450 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.03 % Allowed : 13.79 % Favored : 85.18 % 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: 2.34 (0.25), residues: 1238 helix: 2.67 (0.18), residues: 750 sheet: -0.47 (0.42), residues: 128 loop : -0.08 (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 0.010 0.001 PHE D 117 TYR 0.021 0.001 TYR A 106 ARG 0.002 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 643) hydrogen bonds : angle 4.32771 ( 1890) covalent geometry : bond 0.00281 (10380) covalent geometry : angle 0.47956 (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 135 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.136 Fit side-chains REVERT: A 106 TYR cc_start: 0.7660 (t80) cc_final: 0.7371 (t80) REVERT: A 218 ASN cc_start: 0.8033 (m-40) cc_final: 0.7773 (m-40) REVERT: A 220 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7391 (ptm160) REVERT: B 120 MET cc_start: 0.7526 (mmt) cc_final: 0.6802 (mmt) REVERT: B 180 ARG cc_start: 0.6671 (ttp-110) cc_final: 0.6210 (mtm-85) REVERT: B 214 MET cc_start: 0.7711 (mmt) cc_final: 0.7163 (ttt) REVERT: B 218 ASN cc_start: 0.7935 (t0) cc_final: 0.7709 (t0) REVERT: B 246 GLU cc_start: 0.7451 (tp30) cc_final: 0.6967 (mm-30) REVERT: C 218 ASN cc_start: 0.7957 (m-40) cc_final: 0.7637 (m-40) REVERT: C 252 GLN cc_start: 0.7177 (mm110) cc_final: 0.6913 (mm-40) REVERT: D 120 MET cc_start: 0.7412 (mmt) cc_final: 0.6534 (mmt) REVERT: D 214 MET cc_start: 0.7832 (mmt) cc_final: 0.7457 (ttt) REVERT: D 220 ARG cc_start: 0.6628 (mtm110) cc_final: 0.6102 (mtp-110) REVERT: D 310 ARG cc_start: 0.8042 (tpt170) cc_final: 0.7758 (tpt90) outliers start: 11 outliers final: 9 residues processed: 131 average time/residue: 0.3139 time to fit residues: 53.8994 Evaluate side-chains 133 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 86 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 chunk 81 optimal weight: 0.0980 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.150024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122884 restraints weight = 11077.920| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.71 r_work: 0.3243 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10380 Z= 0.133 Angle : 0.490 5.269 14118 Z= 0.250 Chirality : 0.038 0.143 1558 Planarity : 0.004 0.053 1798 Dihedral : 4.090 25.240 1450 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.03 % Allowed : 13.98 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.25), residues: 1238 helix: 2.65 (0.18), residues: 750 sheet: -0.50 (0.42), residues: 132 loop : -0.10 (0.38), residues: 356 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 0.010 0.001 PHE D 117 TYR 0.022 0.001 TYR A 106 ARG 0.002 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 643) hydrogen bonds : angle 4.36099 ( 1890) covalent geometry : bond 0.00312 (10380) covalent geometry : angle 0.49006 (14118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5752.99 seconds wall clock time: 102 minutes 25.26 seconds (6145.26 seconds total)