Starting phenix.real_space_refine on Sat Jun 7 08:43:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh3_39280/06_2025/8yh3_39280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh3_39280/06_2025/8yh3_39280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yh3_39280/06_2025/8yh3_39280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh3_39280/06_2025/8yh3_39280.map" model { file = "/net/cci-nas-00/data/ceres_data/8yh3_39280/06_2025/8yh3_39280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh3_39280/06_2025/8yh3_39280.cif" } resolution = 3.4 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= -0.004 sd= 1.094 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 5560 2.51 5 N 1462 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8691 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "R" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2198 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1700 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 208} Chain breaks: 2 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'6MD%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 5.16, per 1000 atoms: 0.59 Number of scatterers: 8691 At special positions: 0 Unit cell: (85.47, 123.21, 124.32, 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 1603 8.00 N 1462 7.00 C 5560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 165 " distance=2.02 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.01 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: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 38.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.705A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'R' and resid 10 through 40 Processing helix chain 'R' and resid 41 through 44 Processing helix chain 'R' and resid 45 through 64 Processing helix chain 'R' and resid 64 through 75 Processing helix chain 'R' and resid 79 through 115 removed outlier: 3.735A pdb=" N THR R 115 " --> pdb=" O ARG R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 123 through 144 Processing helix chain 'R' and resid 145 through 148 Processing helix chain 'R' and resid 150 through 154 Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.501A pdb=" N VAL R 170 " --> pdb=" O ARG R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 179 removed outlier: 3.553A pdb=" N MET R 176 " --> pdb=" O ARG R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 185 through 207 Processing helix chain 'R' and resid 225 through 254 Proline residue: R 244 - end of helix Processing helix chain 'R' and resid 259 through 282 removed outlier: 3.862A pdb=" N MET R 275 " --> pdb=" O HIS R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 285 through 295 Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.502A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.548A pdb=" N LYS A 279 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.690A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 349 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.915A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.955A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.847A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.635A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.137A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.897A 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 153 removed outlier: 3.757A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.028A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.409A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.976A 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 278 removed outlier: 6.472A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.391A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.597A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.278A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.555A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.190A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1182 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: 2.38 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1487 1.31 - 1.44: 2371 1.44 - 1.57: 4918 1.57 - 1.69: 0 1.69 - 1.82: 98 Bond restraints: 8874 Sorted by residual: bond pdb=" C ASP A 200 " pdb=" O ASP A 200 " ideal model delta sigma weight residual 1.236 1.297 -0.061 1.22e-02 6.72e+03 2.49e+01 bond pdb=" CA SER R 100 " pdb=" CB SER R 100 " ideal model delta sigma weight residual 1.528 1.456 0.073 1.56e-02 4.11e+03 2.18e+01 bond pdb=" C PHE R 167 " pdb=" O PHE R 167 " ideal model delta sigma weight residual 1.237 1.290 -0.053 1.17e-02 7.31e+03 2.05e+01 bond pdb=" C TYR R 118 " pdb=" O TYR R 118 " ideal model delta sigma weight residual 1.236 1.287 -0.051 1.15e-02 7.56e+03 1.93e+01 bond pdb=" C ILE R 267 " pdb=" O ILE R 267 " ideal model delta sigma weight residual 1.237 1.289 -0.051 1.17e-02 7.31e+03 1.93e+01 ... (remaining 8869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 10756 2.05 - 4.10: 1146 4.10 - 6.15: 103 6.15 - 8.20: 7 8.20 - 10.25: 6 Bond angle restraints: 12018 Sorted by residual: angle pdb=" N PRO G 53 " pdb=" CA PRO G 53 " pdb=" C PRO G 53 " ideal model delta sigma weight residual 111.14 121.39 -10.25 1.56e+00 4.11e-01 4.32e+01 angle pdb=" N GLY B 162 " pdb=" CA GLY B 162 " pdb=" C GLY B 162 " ideal model delta sigma weight residual 114.67 108.01 6.66 1.10e+00 8.26e-01 3.66e+01 angle pdb=" N LEU R 84 " pdb=" CA LEU R 84 " pdb=" C LEU R 84 " ideal model delta sigma weight residual 111.82 105.46 6.36 1.16e+00 7.43e-01 3.01e+01 angle pdb=" C HIS S 35 " pdb=" CA HIS S 35 " pdb=" CB HIS S 35 " ideal model delta sigma weight residual 109.80 101.52 8.28 1.65e+00 3.67e-01 2.52e+01 angle pdb=" N VAL R 121 " pdb=" CA VAL R 121 " pdb=" C VAL R 121 " ideal model delta sigma weight residual 113.42 107.70 5.72 1.17e+00 7.31e-01 2.39e+01 ... (remaining 12013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 4648 15.91 - 31.82: 489 31.82 - 47.73: 106 47.73 - 63.63: 23 63.63 - 79.54: 5 Dihedral angle restraints: 5271 sinusoidal: 2069 harmonic: 3202 Sorted by residual: dihedral pdb=" CD ARG S 67 " pdb=" NE ARG S 67 " pdb=" CZ ARG S 67 " pdb=" NH1 ARG S 67 " ideal model delta sinusoidal sigma weight residual 0.00 75.41 -75.41 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CD ARG R 172 " pdb=" NE ARG R 172 " pdb=" CZ ARG R 172 " pdb=" NH1 ARG R 172 " ideal model delta sinusoidal sigma weight residual 0.00 -52.92 52.92 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CA TYR S 178 " pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta harmonic sigma weight residual 180.00 155.92 24.08 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 5268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1070 0.098 - 0.196: 274 0.196 - 0.294: 28 0.294 - 0.392: 2 0.392 - 0.489: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CA PRO G 53 " pdb=" N PRO G 53 " pdb=" C PRO G 53 " pdb=" CB PRO G 53 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CB VAL R 112 " pdb=" CA VAL R 112 " pdb=" CG1 VAL R 112 " pdb=" CG2 VAL R 112 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 1373 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 6MD R 801 " -0.174 2.00e-02 2.50e+03 7.31e-02 1.47e+02 pdb=" C2 6MD R 801 " 0.008 2.00e-02 2.50e+03 pdb=" C4 6MD R 801 " 0.060 2.00e-02 2.50e+03 pdb=" C5 6MD R 801 " 0.044 2.00e-02 2.50e+03 pdb=" C6 6MD R 801 " -0.002 2.00e-02 2.50e+03 pdb=" C8 6MD R 801 " 0.048 2.00e-02 2.50e+03 pdb=" N1 6MD R 801 " -0.016 2.00e-02 2.50e+03 pdb=" N3 6MD R 801 " 0.049 2.00e-02 2.50e+03 pdb=" N6 6MD R 801 " -0.115 2.00e-02 2.50e+03 pdb=" N7 6MD R 801 " 0.039 2.00e-02 2.50e+03 pdb=" N9 6MD R 801 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG S 67 " -1.060 9.50e-02 1.11e+02 4.75e-01 1.36e+02 pdb=" NE ARG S 67 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG S 67 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG S 67 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG S 67 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 172 " 0.861 9.50e-02 1.11e+02 3.86e-01 9.04e+01 pdb=" NE ARG R 172 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG R 172 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG R 172 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 172 " 0.023 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 232 2.68 - 3.23: 8682 3.23 - 3.79: 13582 3.79 - 4.34: 19393 4.34 - 4.90: 31082 Nonbonded interactions: 72971 Sorted by model distance: nonbonded pdb=" OE1 GLN S 130 " pdb=" OG1 THR S 231 " model vdw 2.121 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.135 3.040 nonbonded pdb=" OG SER S 99 " pdb=" O PRO S 107 " model vdw 2.191 3.040 nonbonded pdb=" O LEU A 249 " pdb=" OG SER A 252 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR A 287 " pdb=" OE1 GLN A 306 " model vdw 2.211 3.040 ... (remaining 72966 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: 0.900 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 21.980 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5706 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 : 0.010 0.073 8877 Z= 0.737 Angle : 1.220 10.252 12024 Z= 0.863 Chirality : 0.081 0.489 1376 Planarity : 0.022 0.475 1498 Dihedral : 13.869 79.543 3196 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.52 % Favored : 95.30 % Rotamer: Outliers : 1.15 % Allowed : 3.36 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.72 (0.25), residues: 1085 helix: 0.37 (0.26), residues: 362 sheet: -0.95 (0.30), residues: 269 loop : -0.72 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP A 211 HIS 0.019 0.004 HIS A 322 PHE 0.041 0.005 PHE A 334 TYR 0.029 0.004 TYR R 292 ARG 0.013 0.001 ARG R 168 Details of bonding type rmsd hydrogen bonds : bond 0.16631 ( 423) hydrogen bonds : angle 6.73890 ( 1182) SS BOND : bond 0.01534 ( 3) SS BOND : angle 2.05241 ( 6) covalent geometry : bond 0.01016 ( 8874) covalent geometry : angle 1.21965 (12018) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 323 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 MET cc_start: 0.6520 (mmp) cc_final: 0.6261 (mmp) REVERT: A 337 ASP cc_start: 0.5559 (m-30) cc_final: 0.5110 (m-30) REVERT: A 354 PHE cc_start: 0.6246 (OUTLIER) cc_final: 0.5566 (m-80) outliers start: 11 outliers final: 0 residues processed: 331 average time/residue: 0.2415 time to fit residues: 104.1092 Evaluate side-chains 184 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 HIS R 249 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 213 HIS A 244 HIS A 255 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.132738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.108190 restraints weight = 22268.645| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 4.38 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8877 Z= 0.167 Angle : 0.695 10.678 12024 Z= 0.365 Chirality : 0.045 0.216 1376 Planarity : 0.005 0.049 1498 Dihedral : 5.131 57.517 1216 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 2.31 % Allowed : 14.38 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.28 (0.26), residues: 1085 helix: 1.02 (0.27), residues: 365 sheet: -0.86 (0.29), residues: 287 loop : -0.62 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.004 0.001 HIS B 183 PHE 0.022 0.002 PHE S 108 TYR 0.022 0.002 TYR S 178 ARG 0.007 0.001 ARG R 206 Details of bonding type rmsd hydrogen bonds : bond 0.05276 ( 423) hydrogen bonds : angle 5.49872 ( 1182) SS BOND : bond 0.01061 ( 3) SS BOND : angle 2.68167 ( 6) covalent geometry : bond 0.00369 ( 8874) covalent geometry : angle 0.69252 (12018) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.8435 (m100) cc_final: 0.8065 (m100) REVERT: B 258 ASP cc_start: 0.6494 (m-30) cc_final: 0.6084 (t0) REVERT: B 262 MET cc_start: 0.7620 (tpt) cc_final: 0.6629 (tpt) REVERT: R 17 THR cc_start: 0.8289 (p) cc_final: 0.8031 (t) REVERT: R 171 MET cc_start: 0.8132 (tpp) cc_final: 0.7555 (tpp) REVERT: R 206 ARG cc_start: 0.8397 (ttt90) cc_final: 0.8134 (tpt-90) REVERT: R 284 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7495 (mmmt) REVERT: A 28 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 53 MET cc_start: 0.6134 (tpp) cc_final: 0.5642 (tpp) REVERT: A 205 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7452 (tmm160) REVERT: A 259 PHE cc_start: 0.9106 (m-80) cc_final: 0.8865 (m-10) REVERT: A 287 TYR cc_start: 0.7445 (t80) cc_final: 0.7241 (t80) REVERT: A 293 SER cc_start: 0.9056 (t) cc_final: 0.8788 (p) REVERT: A 333 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 337 ASP cc_start: 0.8470 (m-30) cc_final: 0.8141 (m-30) REVERT: A 354 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.5640 (m-80) REVERT: S 93 MET cc_start: 0.7785 (mmm) cc_final: 0.7569 (tmm) outliers start: 22 outliers final: 11 residues processed: 242 average time/residue: 0.2319 time to fit residues: 74.9970 Evaluate side-chains 187 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS R 249 ASN A 304 GLN A 322 HIS ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN S 219 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.129305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.105223 restraints weight = 22580.869| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 4.34 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8877 Z= 0.153 Angle : 0.654 10.234 12024 Z= 0.346 Chirality : 0.044 0.225 1376 Planarity : 0.004 0.047 1498 Dihedral : 4.832 54.908 1216 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 2.20 % Allowed : 16.89 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.01 (0.26), residues: 1085 helix: 1.30 (0.28), residues: 370 sheet: -0.80 (0.29), residues: 285 loop : -0.45 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 184 HIS 0.004 0.001 HIS R 95 PHE 0.020 0.002 PHE R 93 TYR 0.015 0.001 TYR S 60 ARG 0.007 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 423) hydrogen bonds : angle 5.18166 ( 1182) SS BOND : bond 0.00368 ( 3) SS BOND : angle 0.65483 ( 6) covalent geometry : bond 0.00341 ( 8874) covalent geometry : angle 0.65433 (12018) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TRP cc_start: 0.8514 (m100) cc_final: 0.8182 (m100) REVERT: B 176 GLN cc_start: 0.8753 (pt0) cc_final: 0.8473 (pt0) REVERT: B 219 ARG cc_start: 0.7624 (ttt-90) cc_final: 0.7373 (mmm-85) REVERT: B 258 ASP cc_start: 0.7055 (m-30) cc_final: 0.6685 (t70) REVERT: R 17 THR cc_start: 0.8296 (p) cc_final: 0.8033 (t) REVERT: A 21 ARG cc_start: 0.8464 (ttm110) cc_final: 0.7683 (ttp80) REVERT: A 28 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 53 MET cc_start: 0.5762 (tpp) cc_final: 0.5127 (tpp) REVERT: A 205 ARG cc_start: 0.8316 (mmm160) cc_final: 0.7373 (tmm160) REVERT: A 287 TYR cc_start: 0.7434 (t80) cc_final: 0.7229 (t80) REVERT: A 354 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.5785 (m-80) REVERT: S 5 VAL cc_start: 0.7536 (t) cc_final: 0.7269 (p) REVERT: S 34 MET cc_start: 0.6930 (mmp) cc_final: 0.5938 (mmp) REVERT: S 93 MET cc_start: 0.7933 (mmm) cc_final: 0.7631 (tmm) outliers start: 21 outliers final: 11 residues processed: 212 average time/residue: 0.2363 time to fit residues: 65.9963 Evaluate side-chains 174 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 36 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN R 44 GLN R 249 ASN A 244 HIS A 256 ASN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.126340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.100958 restraints weight = 22023.559| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 4.48 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8877 Z= 0.164 Angle : 0.666 10.280 12024 Z= 0.346 Chirality : 0.044 0.161 1376 Planarity : 0.004 0.042 1498 Dihedral : 4.711 54.783 1216 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 3.25 % Allowed : 19.73 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.02 (0.26), residues: 1085 helix: 1.39 (0.27), residues: 369 sheet: -0.74 (0.30), residues: 280 loop : -0.53 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 184 HIS 0.004 0.001 HIS R 271 PHE 0.026 0.002 PHE R 50 TYR 0.015 0.002 TYR S 94 ARG 0.004 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 423) hydrogen bonds : angle 5.07373 ( 1182) SS BOND : bond 0.00359 ( 3) SS BOND : angle 0.65186 ( 6) covalent geometry : bond 0.00367 ( 8874) covalent geometry : angle 0.66558 (12018) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.6067 (ttp) cc_final: 0.5789 (ptm) REVERT: B 176 GLN cc_start: 0.8928 (pt0) cc_final: 0.8685 (pt0) REVERT: B 233 CYS cc_start: 0.7315 (t) cc_final: 0.7104 (t) REVERT: B 258 ASP cc_start: 0.7022 (m-30) cc_final: 0.6570 (t0) REVERT: B 262 MET cc_start: 0.7645 (mmm) cc_final: 0.7185 (mmt) REVERT: B 292 PHE cc_start: 0.8133 (m-80) cc_final: 0.7833 (m-80) REVERT: R 17 THR cc_start: 0.8376 (p) cc_final: 0.8119 (t) REVERT: R 184 TRP cc_start: 0.7373 (m-90) cc_final: 0.6860 (m-90) REVERT: A 53 MET cc_start: 0.5517 (tpp) cc_final: 0.4838 (tpp) REVERT: A 205 ARG cc_start: 0.8311 (mmm160) cc_final: 0.7398 (tmm160) REVERT: A 354 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6014 (m-80) REVERT: S 34 MET cc_start: 0.7050 (mmp) cc_final: 0.6047 (mmp) REVERT: S 93 MET cc_start: 0.8211 (mmm) cc_final: 0.7974 (tmm) REVERT: S 94 TYR cc_start: 0.8367 (m-80) cc_final: 0.7866 (m-10) REVERT: S 103 TYR cc_start: 0.7603 (t80) cc_final: 0.7165 (t80) outliers start: 31 outliers final: 19 residues processed: 206 average time/residue: 0.2285 time to fit residues: 62.7100 Evaluate side-chains 178 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN A 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.124482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.100647 restraints weight = 22494.902| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 4.27 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8877 Z= 0.153 Angle : 0.661 10.177 12024 Z= 0.345 Chirality : 0.043 0.174 1376 Planarity : 0.004 0.038 1498 Dihedral : 4.651 54.513 1216 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 3.78 % Allowed : 21.30 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.10 (0.26), residues: 1085 helix: 1.41 (0.27), residues: 376 sheet: -0.68 (0.30), residues: 284 loop : -0.49 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 184 HIS 0.005 0.001 HIS B 225 PHE 0.020 0.002 PHE B 253 TYR 0.022 0.001 TYR S 178 ARG 0.007 0.001 ARG R 206 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 423) hydrogen bonds : angle 5.03390 ( 1182) SS BOND : bond 0.00390 ( 3) SS BOND : angle 0.52937 ( 6) covalent geometry : bond 0.00346 ( 8874) covalent geometry : angle 0.66115 (12018) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6396 (tp) REVERT: B 124 TYR cc_start: 0.8058 (m-80) cc_final: 0.7845 (m-80) REVERT: B 226 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7693 (mp0) REVERT: B 233 CYS cc_start: 0.7271 (t) cc_final: 0.7069 (t) REVERT: B 258 ASP cc_start: 0.7017 (m-30) cc_final: 0.6460 (t0) REVERT: B 292 PHE cc_start: 0.8299 (m-80) cc_final: 0.7925 (m-80) REVERT: R 17 THR cc_start: 0.8396 (p) cc_final: 0.8149 (t) REVERT: R 58 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8003 (t70) REVERT: R 184 TRP cc_start: 0.7377 (m-90) cc_final: 0.6946 (m-90) REVERT: R 206 ARG cc_start: 0.8548 (tpt-90) cc_final: 0.8310 (ttt90) REVERT: R 277 ASN cc_start: 0.7512 (m110) cc_final: 0.7307 (m110) REVERT: R 283 TYR cc_start: 0.8660 (t80) cc_final: 0.8411 (t80) REVERT: R 284 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8066 (mmmt) REVERT: A 29 LYS cc_start: 0.9053 (ptmm) cc_final: 0.8820 (ptmm) REVERT: A 53 MET cc_start: 0.5651 (tpp) cc_final: 0.5075 (tpp) REVERT: A 205 ARG cc_start: 0.8325 (mmm160) cc_final: 0.7353 (tmm160) REVERT: A 354 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6034 (m-80) REVERT: S 103 TYR cc_start: 0.7674 (t80) cc_final: 0.7315 (t80) REVERT: G 47 GLU cc_start: 0.8066 (tp30) cc_final: 0.7849 (tp30) outliers start: 36 outliers final: 20 residues processed: 206 average time/residue: 0.2243 time to fit residues: 62.2689 Evaluate side-chains 187 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 58 ASP Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 275 MET Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 29 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN A 241 ASN A 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.122322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.098487 restraints weight = 22716.697| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 4.31 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8877 Z= 0.166 Angle : 0.686 10.467 12024 Z= 0.353 Chirality : 0.044 0.169 1376 Planarity : 0.004 0.037 1498 Dihedral : 4.724 55.015 1216 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 3.04 % Allowed : 23.92 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.11 (0.26), residues: 1085 helix: 1.48 (0.27), residues: 369 sheet: -0.70 (0.30), residues: 278 loop : -0.50 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.023 0.002 PHE R 50 TYR 0.016 0.001 TYR S 223 ARG 0.006 0.001 ARG R 206 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 423) hydrogen bonds : angle 5.04125 ( 1182) SS BOND : bond 0.00397 ( 3) SS BOND : angle 0.70862 ( 6) covalent geometry : bond 0.00376 ( 8874) covalent geometry : angle 0.68642 (12018) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6399 (tp) REVERT: B 124 TYR cc_start: 0.8047 (m-80) cc_final: 0.7766 (m-80) REVERT: B 226 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7853 (mp0) REVERT: B 292 PHE cc_start: 0.8245 (m-80) cc_final: 0.7667 (m-10) REVERT: R 30 ASN cc_start: 0.7066 (m-40) cc_final: 0.6860 (m-40) REVERT: R 58 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7729 (t70) REVERT: R 173 MET cc_start: 0.7549 (mmm) cc_final: 0.7346 (mpp) REVERT: R 184 TRP cc_start: 0.7543 (m-90) cc_final: 0.6969 (m-90) REVERT: R 283 TYR cc_start: 0.8533 (t80) cc_final: 0.8315 (t80) REVERT: R 284 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8035 (mmmt) REVERT: A 29 LYS cc_start: 0.9073 (ptmm) cc_final: 0.8849 (ptmm) REVERT: A 205 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7319 (tmm160) REVERT: A 208 ARG cc_start: 0.7898 (tpm170) cc_final: 0.7276 (tpp-160) REVERT: A 354 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: S 103 TYR cc_start: 0.7692 (t80) cc_final: 0.7275 (t80) REVERT: G 47 GLU cc_start: 0.8368 (tp30) cc_final: 0.7874 (tp30) outliers start: 29 outliers final: 17 residues processed: 192 average time/residue: 0.2282 time to fit residues: 58.8883 Evaluate side-chains 181 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 58 ASP Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 159 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 26 optimal weight: 0.0470 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.123170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.098605 restraints weight = 22496.645| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 4.40 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.7389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8877 Z= 0.138 Angle : 0.669 10.438 12024 Z= 0.344 Chirality : 0.043 0.191 1376 Planarity : 0.004 0.036 1498 Dihedral : 4.594 54.488 1216 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 2.83 % Allowed : 24.76 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1085 helix: 1.46 (0.28), residues: 376 sheet: -0.56 (0.30), residues: 279 loop : -0.52 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.018 0.002 PHE A 250 TYR 0.023 0.001 TYR S 178 ARG 0.008 0.001 ARG R 206 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 423) hydrogen bonds : angle 4.97672 ( 1182) SS BOND : bond 0.00419 ( 3) SS BOND : angle 0.48458 ( 6) covalent geometry : bond 0.00311 ( 8874) covalent geometry : angle 0.66918 (12018) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6416 (tp) REVERT: B 82 TRP cc_start: 0.8580 (m100) cc_final: 0.8282 (m100) REVERT: B 124 TYR cc_start: 0.7949 (m-80) cc_final: 0.7682 (m-80) REVERT: B 133 VAL cc_start: 0.8220 (t) cc_final: 0.7992 (m) REVERT: B 226 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8020 (mp0) REVERT: B 262 MET cc_start: 0.7290 (mmm) cc_final: 0.6755 (mmt) REVERT: B 267 ASP cc_start: 0.8563 (t0) cc_final: 0.8357 (p0) REVERT: B 292 PHE cc_start: 0.8247 (m-80) cc_final: 0.7738 (m-80) REVERT: R 58 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7852 (t70) REVERT: R 99 MET cc_start: 0.8617 (mmp) cc_final: 0.8407 (mmm) REVERT: R 119 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8349 (mmm-85) REVERT: R 173 MET cc_start: 0.7449 (mmm) cc_final: 0.7238 (mpp) REVERT: R 183 LEU cc_start: 0.8167 (tp) cc_final: 0.7690 (tp) REVERT: R 283 TYR cc_start: 0.8542 (t80) cc_final: 0.8315 (t80) REVERT: R 284 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8093 (mmmt) REVERT: A 29 LYS cc_start: 0.9055 (ptmm) cc_final: 0.8814 (ptmm) REVERT: A 205 ARG cc_start: 0.8343 (mmm160) cc_final: 0.7402 (tmm160) REVERT: A 241 ASN cc_start: 0.4988 (OUTLIER) cc_final: 0.4762 (p0) REVERT: A 354 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: S 43 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8610 (mmmm) REVERT: S 103 TYR cc_start: 0.7671 (t80) cc_final: 0.7323 (t80) REVERT: G 42 GLU cc_start: 0.7625 (pp20) cc_final: 0.7275 (pt0) REVERT: G 47 GLU cc_start: 0.8437 (tp30) cc_final: 0.7873 (tp30) outliers start: 27 outliers final: 17 residues processed: 195 average time/residue: 0.2330 time to fit residues: 60.7691 Evaluate side-chains 182 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 58 ASP Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 163 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 340 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 205 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.122624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.098045 restraints weight = 22567.345| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 4.43 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.7697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8877 Z= 0.152 Angle : 0.690 10.491 12024 Z= 0.355 Chirality : 0.044 0.235 1376 Planarity : 0.004 0.035 1498 Dihedral : 4.771 54.321 1216 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 3.36 % Allowed : 25.08 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1085 helix: 1.50 (0.27), residues: 377 sheet: -0.46 (0.30), residues: 277 loop : -0.58 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.004 0.001 HIS B 225 PHE 0.032 0.002 PHE R 50 TYR 0.019 0.001 TYR R 15 ARG 0.008 0.001 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 423) hydrogen bonds : angle 4.99775 ( 1182) SS BOND : bond 0.00349 ( 3) SS BOND : angle 0.55749 ( 6) covalent geometry : bond 0.00348 ( 8874) covalent geometry : angle 0.69049 (12018) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6386 (tp) REVERT: B 82 TRP cc_start: 0.8626 (m100) cc_final: 0.8348 (m100) REVERT: B 124 TYR cc_start: 0.7941 (m-80) cc_final: 0.7642 (m-80) REVERT: B 133 VAL cc_start: 0.8204 (t) cc_final: 0.7985 (m) REVERT: B 226 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8070 (mp0) REVERT: B 267 ASP cc_start: 0.8672 (t0) cc_final: 0.8437 (p0) REVERT: B 292 PHE cc_start: 0.8333 (m-80) cc_final: 0.7624 (m-10) REVERT: B 297 TRP cc_start: 0.7752 (m100) cc_final: 0.7497 (m100) REVERT: R 15 TYR cc_start: 0.6842 (t80) cc_final: 0.6470 (t80) REVERT: R 58 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8211 (t70) REVERT: R 173 MET cc_start: 0.7460 (mmm) cc_final: 0.7230 (mpp) REVERT: R 183 LEU cc_start: 0.8160 (tp) cc_final: 0.7638 (tp) REVERT: R 283 TYR cc_start: 0.8557 (t80) cc_final: 0.8345 (t80) REVERT: R 284 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8340 (mmmm) REVERT: A 29 LYS cc_start: 0.9057 (ptmm) cc_final: 0.8804 (ptmm) REVERT: A 33 GLU cc_start: 0.6908 (pp20) cc_final: 0.6555 (pp20) REVERT: A 195 HIS cc_start: 0.8243 (t-90) cc_final: 0.7996 (t-90) REVERT: A 205 ARG cc_start: 0.8354 (mmm160) cc_final: 0.7427 (tmm160) REVERT: A 208 ARG cc_start: 0.7916 (tpm170) cc_final: 0.7396 (tpp-160) REVERT: A 354 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: S 19 LYS cc_start: 0.8679 (mttm) cc_final: 0.8472 (mmmt) REVERT: S 34 MET cc_start: 0.6468 (mmm) cc_final: 0.5719 (mmm) REVERT: S 42 GLU cc_start: 0.9218 (pm20) cc_final: 0.8962 (pm20) REVERT: S 43 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8534 (mmmm) REVERT: S 103 TYR cc_start: 0.7759 (t80) cc_final: 0.7371 (t80) REVERT: S 137 VAL cc_start: 0.7942 (p) cc_final: 0.7722 (p) REVERT: S 207 LEU cc_start: 0.9406 (tt) cc_final: 0.8938 (pt) REVERT: S 208 GLU cc_start: 0.8926 (pm20) cc_final: 0.8154 (pm20) REVERT: G 47 GLU cc_start: 0.8350 (tp30) cc_final: 0.7731 (tp30) outliers start: 32 outliers final: 19 residues processed: 190 average time/residue: 0.2277 time to fit residues: 58.2986 Evaluate side-chains 186 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 58 ASP Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 163 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 96 optimal weight: 0.0970 chunk 107 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.117742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.092691 restraints weight = 22861.286| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.48 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.8230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 8877 Z= 0.248 Angle : 0.803 13.394 12024 Z= 0.409 Chirality : 0.047 0.232 1376 Planarity : 0.004 0.036 1498 Dihedral : 5.433 58.023 1216 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.65 % Rotamer: Outliers : 2.94 % Allowed : 25.60 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.13 (0.26), residues: 1085 helix: 1.18 (0.27), residues: 370 sheet: -0.74 (0.30), residues: 282 loop : -0.62 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 128 HIS 0.006 0.002 HIS R 95 PHE 0.018 0.002 PHE B 253 TYR 0.031 0.002 TYR S 223 ARG 0.006 0.001 ARG A 15 Details of bonding type rmsd hydrogen bonds : bond 0.05844 ( 423) hydrogen bonds : angle 5.37150 ( 1182) SS BOND : bond 0.00280 ( 3) SS BOND : angle 0.86968 ( 6) covalent geometry : bond 0.00568 ( 8874) covalent geometry : angle 0.80322 (12018) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6446 (tp) REVERT: B 82 TRP cc_start: 0.8711 (m100) cc_final: 0.8339 (m100) REVERT: B 211 TRP cc_start: 0.5165 (OUTLIER) cc_final: 0.4235 (m-10) REVERT: B 226 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8168 (mm-30) REVERT: B 292 PHE cc_start: 0.8441 (m-80) cc_final: 0.7994 (m-10) REVERT: R 40 ASN cc_start: 0.8139 (m110) cc_final: 0.7720 (t0) REVERT: R 58 ASP cc_start: 0.8299 (t0) cc_final: 0.8032 (t70) REVERT: R 173 MET cc_start: 0.7736 (mmm) cc_final: 0.7431 (tpp) REVERT: A 29 LYS cc_start: 0.9083 (ptmm) cc_final: 0.8815 (ptmm) REVERT: A 185 VAL cc_start: 0.8002 (m) cc_final: 0.7751 (p) REVERT: A 195 HIS cc_start: 0.8170 (t-90) cc_final: 0.7682 (t-90) REVERT: A 208 ARG cc_start: 0.8180 (tpm170) cc_final: 0.7588 (tpp-160) REVERT: A 247 MET cc_start: 0.8404 (mtp) cc_final: 0.8146 (mtm) REVERT: A 354 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6660 (m-80) REVERT: S 34 MET cc_start: 0.6611 (mmm) cc_final: 0.5436 (mmm) REVERT: S 43 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8712 (mmmm) REVERT: S 89 GLU cc_start: 0.8220 (pm20) cc_final: 0.7617 (pm20) REVERT: S 180 MET cc_start: 0.8339 (mmm) cc_final: 0.7919 (mmm) REVERT: S 208 GLU cc_start: 0.9056 (pm20) cc_final: 0.8481 (pm20) outliers start: 28 outliers final: 20 residues processed: 189 average time/residue: 0.2528 time to fit residues: 64.6501 Evaluate side-chains 180 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 159 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 0.0670 chunk 88 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 48 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.123428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.098589 restraints weight = 22189.278| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 4.37 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.8397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8877 Z= 0.146 Angle : 0.754 11.879 12024 Z= 0.381 Chirality : 0.044 0.201 1376 Planarity : 0.004 0.035 1498 Dihedral : 4.914 56.828 1216 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.10 % Allowed : 27.60 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.07 (0.26), residues: 1085 helix: 1.28 (0.27), residues: 376 sheet: -0.66 (0.30), residues: 274 loop : -0.70 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 242 HIS 0.003 0.001 HIS R 95 PHE 0.032 0.002 PHE R 50 TYR 0.037 0.002 TYR R 264 ARG 0.005 0.000 ARG R 119 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 423) hydrogen bonds : angle 5.05250 ( 1182) SS BOND : bond 0.00517 ( 3) SS BOND : angle 0.48283 ( 6) covalent geometry : bond 0.00330 ( 8874) covalent geometry : angle 0.75409 (12018) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6448 (tp) REVERT: B 79 LEU cc_start: 0.9023 (tp) cc_final: 0.8811 (tp) REVERT: B 133 VAL cc_start: 0.8219 (t) cc_final: 0.7988 (m) REVERT: B 226 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7907 (mp0) REVERT: B 297 TRP cc_start: 0.7637 (m100) cc_final: 0.7425 (m100) REVERT: R 40 ASN cc_start: 0.8151 (m110) cc_final: 0.7545 (t0) REVERT: R 58 ASP cc_start: 0.8404 (t0) cc_final: 0.8137 (t70) REVERT: R 183 LEU cc_start: 0.8473 (tp) cc_final: 0.7965 (tp) REVERT: R 184 TRP cc_start: 0.7394 (m-90) cc_final: 0.6884 (m-90) REVERT: A 185 VAL cc_start: 0.7940 (m) cc_final: 0.7710 (p) REVERT: A 208 ARG cc_start: 0.8258 (tpm170) cc_final: 0.7677 (tpp-160) REVERT: A 247 MET cc_start: 0.8439 (mtp) cc_final: 0.8200 (mtm) REVERT: A 354 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6664 (m-80) REVERT: S 43 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8634 (mmmm) REVERT: S 87 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7614 (mtm-85) REVERT: G 42 GLU cc_start: 0.7727 (pp20) cc_final: 0.7151 (pt0) REVERT: G 47 GLU cc_start: 0.7936 (tp30) cc_final: 0.7223 (tp30) outliers start: 20 outliers final: 13 residues processed: 185 average time/residue: 0.2094 time to fit residues: 52.8459 Evaluate side-chains 170 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 159 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 107 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.121884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.097468 restraints weight = 22488.687| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 4.39 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.8523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8877 Z= 0.160 Angle : 0.762 12.796 12024 Z= 0.383 Chirality : 0.045 0.231 1376 Planarity : 0.004 0.034 1498 Dihedral : 4.950 56.394 1216 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.99 % Allowed : 27.70 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.16 (0.26), residues: 1085 helix: 1.27 (0.27), residues: 373 sheet: -0.89 (0.29), residues: 285 loop : -0.65 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 82 HIS 0.003 0.001 HIS R 95 PHE 0.018 0.002 PHE R 93 TYR 0.031 0.002 TYR R 15 ARG 0.009 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04837 ( 423) hydrogen bonds : angle 5.13717 ( 1182) SS BOND : bond 0.00426 ( 3) SS BOND : angle 0.58300 ( 6) covalent geometry : bond 0.00367 ( 8874) covalent geometry : angle 0.76167 (12018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4303.05 seconds wall clock time: 75 minutes 31.24 seconds (4531.24 seconds total)