Starting phenix.real_space_refine on Tue Apr 29 16:43:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ij3_35463/04_2025/8ij3_35463.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ij3_35463/04_2025/8ij3_35463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ij3_35463/04_2025/8ij3_35463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ij3_35463/04_2025/8ij3_35463.map" model { file = "/net/cci-nas-00/data/ceres_data/8ij3_35463/04_2025/8ij3_35463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ij3_35463/04_2025/8ij3_35463.cif" } resolution = 3.28 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= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5572 2.51 5 N 1507 2.21 5 O 1627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8772 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2253 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 10, 'TRANS': 281} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1701 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Time building chain proxies: 5.80, per 1000 atoms: 0.66 Number of scatterers: 8772 At special positions: 0 Unit cell: (90.1, 120.7, 135.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1627 8.00 N 1507 7.00 C 5572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 35.5% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.700A pdb=" N VAL A 27 " --> pdb=" O ASP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 54 removed outlier: 3.875A pdb=" N VAL A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.914A pdb=" N LEU A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.666A pdb=" N LEU A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 131 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.515A pdb=" N ASN A 137 " --> pdb=" O HIS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 160 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 191 through 218 removed outlier: 4.461A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 261 removed outlier: 3.576A pdb=" N LYS A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 270 through 284 removed outlier: 4.040A pdb=" N LEU A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 Proline residue: A 291 - end of helix removed outlier: 3.506A pdb=" N TYR A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.921A pdb=" N ILE C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.081A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.683A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 removed outlier: 3.738A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 329 No H-bonds generated for 'chain 'C' and resid 327 through 329' Processing helix chain 'C' and resid 330 through 352 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.550A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.643A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.645A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.969A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.031A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.623A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.365A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.710A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 186 removed outlier: 3.645A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.049A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.049A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.758A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 143 through 147 425 hydrogen bonds defined for protein. 1179 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: 2.54 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2313 1.33 - 1.45: 1766 1.45 - 1.58: 4784 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 8958 Sorted by residual: bond pdb=" N VAL C 50 " pdb=" CA VAL C 50 " ideal model delta sigma weight residual 1.462 1.500 -0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" N GLY A 96 " pdb=" CA GLY A 96 " ideal model delta sigma weight residual 1.446 1.477 -0.031 9.70e-03 1.06e+04 1.04e+01 bond pdb=" N LYS C 51 " pdb=" CA LYS C 51 " ideal model delta sigma weight residual 1.458 1.499 -0.042 1.33e-02 5.65e+03 9.92e+00 bond pdb=" CA CYS C 351 " pdb=" C CYS C 351 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.36e-02 5.41e+03 9.10e+00 bond pdb=" CG HIS C 188 " pdb=" CD2 HIS C 188 " ideal model delta sigma weight residual 1.354 1.321 0.033 1.10e-02 8.26e+03 8.76e+00 ... (remaining 8953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.23: 12106 7.23 - 14.46: 24 14.46 - 21.70: 7 21.70 - 28.93: 4 28.93 - 36.16: 1 Bond angle restraints: 12142 Sorted by residual: angle pdb=" C PHE A 296 " pdb=" CA PHE A 296 " pdb=" CB PHE A 296 " ideal model delta sigma weight residual 111.23 75.07 36.16 1.63e+00 3.76e-01 4.92e+02 angle pdb=" N TYR C 290 " pdb=" CA TYR C 290 " pdb=" C TYR C 290 " ideal model delta sigma weight residual 108.31 135.54 -27.23 1.52e+00 4.33e-01 3.21e+02 angle pdb=" N PHE A 296 " pdb=" CA PHE A 296 " pdb=" C PHE A 296 " ideal model delta sigma weight residual 113.38 133.90 -20.52 1.17e+00 7.31e-01 3.08e+02 angle pdb=" N PHE A 244 " pdb=" CA PHE A 244 " pdb=" C PHE A 244 " ideal model delta sigma weight residual 113.18 127.57 -14.39 1.21e+00 6.83e-01 1.41e+02 angle pdb=" N HIS A 184 " pdb=" CA HIS A 184 " pdb=" C HIS A 184 " ideal model delta sigma weight residual 110.80 85.54 25.26 2.13e+00 2.20e-01 1.41e+02 ... (remaining 12137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4529 17.84 - 35.68: 574 35.68 - 53.52: 173 53.52 - 71.36: 23 71.36 - 89.20: 10 Dihedral angle restraints: 5309 sinusoidal: 2024 harmonic: 3285 Sorted by residual: dihedral pdb=" C PHE A 296 " pdb=" N PHE A 296 " pdb=" CA PHE A 296 " pdb=" CB PHE A 296 " ideal model delta harmonic sigma weight residual -122.60 -91.67 -30.93 0 2.50e+00 1.60e-01 1.53e+02 dihedral pdb=" C GLU C 289 " pdb=" N GLU C 289 " pdb=" CA GLU C 289 " pdb=" CB GLU C 289 " ideal model delta harmonic sigma weight residual -122.60 -150.67 28.07 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" N GLU C 289 " pdb=" C GLU C 289 " pdb=" CA GLU C 289 " pdb=" CB GLU C 289 " ideal model delta harmonic sigma weight residual 122.80 148.64 -25.84 0 2.50e+00 1.60e-01 1.07e+02 ... (remaining 5306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 1362 0.270 - 0.540: 10 0.540 - 0.811: 0 0.811 - 1.081: 0 1.081 - 1.351: 3 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CA GLU C 289 " pdb=" N GLU C 289 " pdb=" C GLU C 289 " pdb=" CB GLU C 289 " both_signs ideal model delta sigma weight residual False 2.51 1.16 1.35 2.00e-01 2.50e+01 4.56e+01 chirality pdb=" CA TYR C 290 " pdb=" N TYR C 290 " pdb=" C TYR C 290 " pdb=" CB TYR C 290 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.48e+01 chirality pdb=" CA PHE A 244 " pdb=" N PHE A 244 " pdb=" C PHE A 244 " pdb=" CB PHE A 244 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.09 2.00e-01 2.50e+01 2.94e+01 ... (remaining 1372 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 98 " 0.064 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO A 99 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.54e+00 pdb=" N PRO B 39 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 191 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C ALA A 191 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA A 191 " 0.015 2.00e-02 2.50e+03 pdb=" N MET A 192 " 0.013 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 177 2.67 - 3.22: 8004 3.22 - 3.78: 13155 3.78 - 4.34: 17210 4.34 - 4.90: 29914 Nonbonded interactions: 68460 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.107 3.040 nonbonded pdb=" NE2 HIS C 188 " pdb=" NE2 HIS C 195 " model vdw 2.127 3.200 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.190 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.221 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.224 3.040 ... (remaining 68455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 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: 23.610 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8963 Z= 0.238 Angle : 1.084 36.159 12152 Z= 0.656 Chirality : 0.079 1.351 1375 Planarity : 0.005 0.097 1546 Dihedral : 17.305 89.197 3170 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.71 % Allowed : 28.77 % Favored : 69.52 % Cbeta Deviations : 1.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1118 helix: 1.53 (0.28), residues: 372 sheet: -0.32 (0.30), residues: 276 loop : -1.31 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 93 HIS 0.005 0.001 HIS A 9 PHE 0.017 0.001 PHE A 95 TYR 0.023 0.001 TYR C 290 ARG 0.014 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.13855 ( 415) hydrogen bonds : angle 5.47879 ( 1179) SS BOND : bond 0.00552 ( 5) SS BOND : angle 1.18823 ( 10) covalent geometry : bond 0.00389 ( 8958) covalent geometry : angle 1.08374 (12142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.913 Fit side-chains REVERT: A 213 TRP cc_start: 0.8030 (t60) cc_final: 0.7519 (t-100) REVERT: B 175 GLN cc_start: 0.8145 (pp30) cc_final: 0.7932 (pp30) REVERT: C 350 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8040 (t0) outliers start: 16 outliers final: 5 residues processed: 147 average time/residue: 0.2589 time to fit residues: 49.7960 Evaluate side-chains 134 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 189 HIS S 130 GLN S 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.146868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.107832 restraints weight = 11284.276| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.46 r_work: 0.3022 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8963 Z= 0.125 Angle : 0.557 9.480 12152 Z= 0.293 Chirality : 0.042 0.180 1375 Planarity : 0.004 0.053 1546 Dihedral : 5.200 56.201 1238 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.96 % Allowed : 26.42 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1118 helix: 2.08 (0.28), residues: 368 sheet: -0.28 (0.30), residues: 278 loop : -1.13 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS C 188 PHE 0.013 0.001 PHE A 277 TYR 0.017 0.001 TYR S 178 ARG 0.007 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 415) hydrogen bonds : angle 4.15089 ( 1179) SS BOND : bond 0.00510 ( 5) SS BOND : angle 2.68417 ( 10) covalent geometry : bond 0.00283 ( 8958) covalent geometry : angle 0.55210 (12142) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.926 Fit side-chains REVERT: A 63 ARG cc_start: 0.8778 (mmt180) cc_final: 0.8516 (mmm-85) REVERT: A 84 MET cc_start: 0.7310 (ptp) cc_final: 0.7018 (ptp) REVERT: A 213 TRP cc_start: 0.8168 (t60) cc_final: 0.7681 (t-100) REVERT: A 288 MET cc_start: 0.8145 (ttp) cc_final: 0.7925 (ttp) REVERT: A 295 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.6149 (m-80) REVERT: B 234 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8757 (m-80) REVERT: B 260 GLU cc_start: 0.7658 (tt0) cc_final: 0.7439 (tt0) REVERT: B 268 ASN cc_start: 0.8520 (t0) cc_final: 0.8302 (t0) REVERT: B 338 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8582 (mm) outliers start: 37 outliers final: 16 residues processed: 171 average time/residue: 0.2328 time to fit residues: 53.3187 Evaluate side-chains 153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 189 HIS A 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.100187 restraints weight = 11499.531| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.48 r_work: 0.2913 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 8963 Z= 0.303 Angle : 0.665 10.204 12152 Z= 0.353 Chirality : 0.046 0.154 1375 Planarity : 0.005 0.054 1546 Dihedral : 5.382 61.516 1227 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.78 % Allowed : 26.10 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1118 helix: 1.66 (0.27), residues: 379 sheet: -0.45 (0.31), residues: 278 loop : -1.56 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 47 HIS 0.011 0.002 HIS A 189 PHE 0.022 0.002 PHE B 199 TYR 0.019 0.002 TYR S 178 ARG 0.006 0.001 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.05749 ( 415) hydrogen bonds : angle 4.46440 ( 1179) SS BOND : bond 0.00746 ( 5) SS BOND : angle 2.10413 ( 10) covalent geometry : bond 0.00747 ( 8958) covalent geometry : angle 0.66230 (12142) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 232 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6864 (t80) REVERT: B 234 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8756 (m-80) REVERT: B 268 ASN cc_start: 0.8595 (t0) cc_final: 0.8362 (t0) REVERT: B 338 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8630 (mm) REVERT: S 34 MET cc_start: 0.8812 (mmm) cc_final: 0.8611 (mmt) REVERT: S 190 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8294 (ptt90) REVERT: S 203 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8889 (p) outliers start: 54 outliers final: 31 residues processed: 173 average time/residue: 0.2309 time to fit residues: 53.8196 Evaluate side-chains 168 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.144830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105857 restraints weight = 11246.940| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.46 r_work: 0.3007 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8963 Z= 0.116 Angle : 0.562 10.802 12152 Z= 0.292 Chirality : 0.041 0.135 1375 Planarity : 0.004 0.048 1546 Dihedral : 4.965 63.523 1227 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.85 % Allowed : 27.27 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1118 helix: 2.03 (0.27), residues: 374 sheet: -0.34 (0.30), residues: 280 loop : -1.33 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS A 9 PHE 0.013 0.001 PHE A 277 TYR 0.016 0.001 TYR S 178 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 415) hydrogen bonds : angle 4.07135 ( 1179) SS BOND : bond 0.00793 ( 5) SS BOND : angle 3.14225 ( 10) covalent geometry : bond 0.00260 ( 8958) covalent geometry : angle 0.55474 (12142) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.926 Fit side-chains REVERT: A 213 TRP cc_start: 0.8188 (t60) cc_final: 0.7704 (t-100) REVERT: A 232 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6850 (t80) REVERT: A 273 ASP cc_start: 0.8097 (t0) cc_final: 0.7073 (p0) REVERT: A 295 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.6158 (m-80) REVERT: B 234 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8755 (m-80) REVERT: B 268 ASN cc_start: 0.8681 (t0) cc_final: 0.8414 (t0) REVERT: B 338 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8606 (mm) REVERT: G 21 MET cc_start: 0.7277 (tpp) cc_final: 0.7049 (tpp) REVERT: S 190 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8099 (ptt90) outliers start: 36 outliers final: 15 residues processed: 164 average time/residue: 0.2330 time to fit residues: 51.0264 Evaluate side-chains 155 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.106174 restraints weight = 11453.420| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.46 r_work: 0.2988 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8963 Z= 0.159 Angle : 0.564 11.478 12152 Z= 0.296 Chirality : 0.042 0.134 1375 Planarity : 0.004 0.048 1546 Dihedral : 4.983 64.513 1227 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.81 % Allowed : 25.67 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1118 helix: 2.05 (0.27), residues: 373 sheet: -0.36 (0.30), residues: 280 loop : -1.29 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS A 9 PHE 0.015 0.001 PHE A 277 TYR 0.016 0.001 TYR S 178 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 415) hydrogen bonds : angle 4.10049 ( 1179) SS BOND : bond 0.00521 ( 5) SS BOND : angle 2.54109 ( 10) covalent geometry : bond 0.00379 ( 8958) covalent geometry : angle 0.55930 (12142) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7533 (ptp) cc_final: 0.7309 (ptp) REVERT: A 215 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8535 (mp) REVERT: A 232 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6679 (t80) REVERT: A 295 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: B 234 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8710 (m-80) REVERT: B 268 ASN cc_start: 0.8587 (t0) cc_final: 0.8316 (t0) REVERT: B 338 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8491 (mm) REVERT: C 283 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7950 (tt) REVERT: C 315 ASP cc_start: 0.8179 (p0) cc_final: 0.7957 (p0) REVERT: G 21 MET cc_start: 0.7326 (tpp) cc_final: 0.7065 (tpp) REVERT: S 190 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8177 (ptt90) outliers start: 45 outliers final: 26 residues processed: 171 average time/residue: 0.2330 time to fit residues: 53.3852 Evaluate side-chains 167 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.145207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106282 restraints weight = 11326.949| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.47 r_work: 0.3014 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8963 Z= 0.122 Angle : 0.545 11.996 12152 Z= 0.284 Chirality : 0.041 0.140 1375 Planarity : 0.004 0.046 1546 Dihedral : 4.866 65.436 1227 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.39 % Allowed : 26.10 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1118 helix: 2.10 (0.27), residues: 373 sheet: -0.26 (0.30), residues: 285 loop : -1.24 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS A 9 PHE 0.015 0.001 PHE A 277 TYR 0.015 0.001 TYR S 178 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 415) hydrogen bonds : angle 3.99198 ( 1179) SS BOND : bond 0.00489 ( 5) SS BOND : angle 1.64378 ( 10) covalent geometry : bond 0.00278 ( 8958) covalent geometry : angle 0.54365 (12142) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8683 (mm) cc_final: 0.8470 (mm) REVERT: A 213 TRP cc_start: 0.8135 (t60) cc_final: 0.7678 (t-100) REVERT: A 215 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8467 (mp) REVERT: A 232 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6629 (t80) REVERT: A 273 ASP cc_start: 0.8033 (t0) cc_final: 0.7050 (p0) REVERT: A 295 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.6109 (m-80) REVERT: B 234 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8688 (m-80) REVERT: B 268 ASN cc_start: 0.8583 (t0) cc_final: 0.8304 (t0) REVERT: B 338 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8475 (mm) REVERT: C 283 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7863 (tt) REVERT: C 315 ASP cc_start: 0.8199 (p0) cc_final: 0.7947 (p0) REVERT: G 21 MET cc_start: 0.7318 (tpp) cc_final: 0.7000 (tpp) REVERT: S 13 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8071 (mm-40) REVERT: S 190 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8109 (ptt90) outliers start: 41 outliers final: 24 residues processed: 169 average time/residue: 0.2351 time to fit residues: 53.2215 Evaluate side-chains 168 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.145758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.106969 restraints weight = 11373.899| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.47 r_work: 0.3026 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 0.029 8963 Z= 0.116 Angle : 0.541 12.784 12152 Z= 0.281 Chirality : 0.041 0.149 1375 Planarity : 0.004 0.045 1546 Dihedral : 4.784 66.057 1227 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.28 % Allowed : 26.10 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1118 helix: 2.04 (0.27), residues: 380 sheet: -0.19 (0.30), residues: 285 loop : -1.21 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS A 9 PHE 0.014 0.001 PHE C 354 TYR 0.017 0.001 TYR C 302 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 415) hydrogen bonds : angle 3.93829 ( 1179) SS BOND : bond 0.00410 ( 5) SS BOND : angle 1.47062 ( 10) covalent geometry : bond 0.00264 ( 8958) covalent geometry : angle 0.54003 (12142) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8671 (mm) cc_final: 0.8448 (mm) REVERT: A 213 TRP cc_start: 0.8145 (t60) cc_final: 0.7857 (t-100) REVERT: A 215 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8277 (mp) REVERT: A 232 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6685 (t80) REVERT: A 273 ASP cc_start: 0.8074 (t0) cc_final: 0.7075 (p0) REVERT: B 234 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8701 (m-80) REVERT: B 268 ASN cc_start: 0.8572 (t0) cc_final: 0.8291 (t0) REVERT: B 338 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8474 (mm) REVERT: C 283 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7928 (tt) REVERT: C 315 ASP cc_start: 0.8101 (p0) cc_final: 0.7882 (p0) REVERT: G 21 MET cc_start: 0.7492 (tpp) cc_final: 0.7140 (tpp) REVERT: S 13 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8069 (mm-40) REVERT: S 190 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8057 (ptt90) outliers start: 40 outliers final: 26 residues processed: 172 average time/residue: 0.2302 time to fit residues: 53.0863 Evaluate side-chains 168 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105532 restraints weight = 11617.994| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.54 r_work: 0.2969 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8963 Z= 0.177 Angle : 0.595 13.218 12152 Z= 0.309 Chirality : 0.042 0.153 1375 Planarity : 0.004 0.046 1546 Dihedral : 4.975 65.575 1227 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 4.71 % Allowed : 25.67 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1118 helix: 2.04 (0.27), residues: 374 sheet: -0.24 (0.30), residues: 286 loop : -1.23 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 9 PHE 0.015 0.002 PHE A 38 TYR 0.018 0.002 TYR C 230 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 415) hydrogen bonds : angle 4.09378 ( 1179) SS BOND : bond 0.00545 ( 5) SS BOND : angle 1.82257 ( 10) covalent geometry : bond 0.00429 ( 8958) covalent geometry : angle 0.59249 (12142) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8722 (mm) cc_final: 0.8505 (mm) REVERT: A 213 TRP cc_start: 0.8194 (t60) cc_final: 0.7691 (t-100) REVERT: A 215 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8467 (mp) REVERT: A 232 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6691 (t80) REVERT: A 273 ASP cc_start: 0.8213 (t0) cc_final: 0.7059 (p0) REVERT: B 234 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8761 (m-80) REVERT: B 268 ASN cc_start: 0.8647 (t0) cc_final: 0.8371 (t0) REVERT: B 338 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8520 (mm) REVERT: C 283 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7902 (tt) REVERT: C 302 TYR cc_start: 0.8459 (t80) cc_final: 0.8256 (t80) REVERT: G 21 MET cc_start: 0.7510 (tpp) cc_final: 0.7154 (tpp) REVERT: S 190 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8073 (ptt90) outliers start: 44 outliers final: 34 residues processed: 168 average time/residue: 0.2488 time to fit residues: 56.3265 Evaluate side-chains 171 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.146164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107357 restraints weight = 11562.353| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.50 r_work: 0.3005 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 0.029 8963 Z= 0.133 Angle : 0.575 13.227 12152 Z= 0.297 Chirality : 0.042 0.180 1375 Planarity : 0.004 0.045 1546 Dihedral : 4.913 66.049 1227 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 4.39 % Allowed : 26.20 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1118 helix: 2.06 (0.27), residues: 374 sheet: -0.19 (0.30), residues: 286 loop : -1.19 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.005 0.001 HIS A 9 PHE 0.014 0.001 PHE C 354 TYR 0.018 0.001 TYR C 230 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 415) hydrogen bonds : angle 4.00671 ( 1179) SS BOND : bond 0.00438 ( 5) SS BOND : angle 1.14056 ( 10) covalent geometry : bond 0.00309 ( 8958) covalent geometry : angle 0.57384 (12142) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8719 (mm) cc_final: 0.8513 (mm) REVERT: A 213 TRP cc_start: 0.8170 (t60) cc_final: 0.7806 (t-100) REVERT: A 215 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8313 (mp) REVERT: A 232 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6657 (t80) REVERT: A 273 ASP cc_start: 0.8329 (t0) cc_final: 0.7007 (p0) REVERT: B 175 GLN cc_start: 0.8201 (pp30) cc_final: 0.7936 (pp30) REVERT: B 234 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8681 (m-80) REVERT: B 268 ASN cc_start: 0.8628 (t0) cc_final: 0.8351 (t0) REVERT: B 338 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8499 (mm) REVERT: C 283 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7935 (tt) REVERT: C 302 TYR cc_start: 0.8494 (t80) cc_final: 0.8280 (t80) REVERT: G 21 MET cc_start: 0.7560 (tpp) cc_final: 0.7172 (tpp) REVERT: S 190 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8155 (ptt180) outliers start: 41 outliers final: 32 residues processed: 163 average time/residue: 0.2487 time to fit residues: 53.9326 Evaluate side-chains 169 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 42 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.143722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104981 restraints weight = 11412.485| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.50 r_work: 0.2999 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8963 Z= 0.148 Angle : 0.582 13.521 12152 Z= 0.301 Chirality : 0.042 0.163 1375 Planarity : 0.004 0.045 1546 Dihedral : 4.930 66.069 1227 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 4.71 % Allowed : 26.31 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1118 helix: 2.13 (0.27), residues: 368 sheet: -0.19 (0.30), residues: 286 loop : -1.16 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 93 HIS 0.005 0.001 HIS A 9 PHE 0.017 0.001 PHE A 38 TYR 0.018 0.001 TYR C 230 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 415) hydrogen bonds : angle 4.06853 ( 1179) SS BOND : bond 0.00468 ( 5) SS BOND : angle 1.06858 ( 10) covalent geometry : bond 0.00351 ( 8958) covalent geometry : angle 0.58135 (12142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8742 (mm) cc_final: 0.8508 (mm) REVERT: A 213 TRP cc_start: 0.8160 (t60) cc_final: 0.7655 (t-100) REVERT: A 215 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8310 (mp) REVERT: A 232 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6650 (t80) REVERT: A 273 ASP cc_start: 0.8367 (t0) cc_final: 0.7084 (p0) REVERT: B 175 GLN cc_start: 0.8196 (pp30) cc_final: 0.7952 (pp30) REVERT: B 234 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8747 (m-80) REVERT: B 268 ASN cc_start: 0.8637 (t0) cc_final: 0.8347 (t0) REVERT: B 338 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8500 (mm) REVERT: C 283 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7916 (tt) REVERT: G 21 MET cc_start: 0.7584 (tpp) cc_final: 0.7200 (tpp) REVERT: S 190 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7995 (ptt90) outliers start: 44 outliers final: 36 residues processed: 168 average time/residue: 0.2517 time to fit residues: 57.4152 Evaluate side-chains 174 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 101 optimal weight: 0.0270 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.0270 chunk 53 optimal weight: 0.9980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.148938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110203 restraints weight = 11522.346| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.49 r_work: 0.3053 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8963 Z= 0.107 Angle : 0.561 13.595 12152 Z= 0.289 Chirality : 0.041 0.173 1375 Planarity : 0.004 0.044 1546 Dihedral : 4.775 67.097 1227 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % Rotamer: Outliers : 3.74 % Allowed : 27.27 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1118 helix: 2.19 (0.27), residues: 368 sheet: -0.08 (0.30), residues: 283 loop : -1.11 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 93 HIS 0.005 0.001 HIS A 9 PHE 0.016 0.001 PHE C 354 TYR 0.018 0.001 TYR C 230 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 415) hydrogen bonds : angle 3.92423 ( 1179) SS BOND : bond 0.00357 ( 5) SS BOND : angle 0.70895 ( 10) covalent geometry : bond 0.00235 ( 8958) covalent geometry : angle 0.56075 (12142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4502.49 seconds wall clock time: 78 minutes 23.17 seconds (4703.17 seconds total)