Starting phenix.real_space_refine on Wed Jan 15 17:14:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh3_39280/01_2025/8yh3_39280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh3_39280/01_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_39280/01_2025/8yh3_39280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh3_39280/01_2025/8yh3_39280.map" model { file = "/net/cci-nas-00/data/ceres_data/8yh3_39280/01_2025/8yh3_39280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh3_39280/01_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 4.95, per 1000 atoms: 0.57 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: 2.42 Conformation dependent library (CDL) restraints added in 1.0 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: 0.82 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: 2.50 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 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: 10759 2.05 - 4.10: 1146 4.10 - 6.15: 99 6.15 - 8.20: 8 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: 490 31.82 - 47.73: 105 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=" C1' 6MD R 801 " pdb=" C2' 6MD R 801 " pdb=" C3' 6MD R 801 " pdb=" C4' 6MD R 801 " ideal model delta sinusoidal sigma weight residual -35.00 2.40 -37.40 1 8.00e+00 1.56e-02 3.08e+01 ... (remaining 5268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1070 0.098 - 0.196: 275 0.196 - 0.294: 27 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: 0.730 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.280 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- 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 8874 Z= 0.654 Angle : 1.218 10.252 12018 Z= 0.865 Chirality : 0.081 0.489 1376 Planarity : 0.022 0.475 1498 Dihedral : 13.857 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 *********************** 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 : 0.938 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: 0.2763 time to fit residues: 119.0524 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 : 1.002 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.133026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.108697 restraints weight = 22272.272| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 4.37 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8874 Z= 0.236 Angle : 0.691 10.863 12018 Z= 0.365 Chirality : 0.045 0.225 1376 Planarity : 0.005 0.049 1498 Dihedral : 5.072 57.493 1216 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 2.41 % Allowed : 14.48 % Favored : 83.11 % 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: 1.04 (0.27), residues: 365 sheet: -0.85 (0.29), residues: 287 loop : -0.63 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.021 0.002 PHE S 108 TYR 0.022 0.002 TYR S 178 ARG 0.007 0.001 ARG R 206 *********************** 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 245 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 1.129 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 82 TRP cc_start: 0.8441 (m100) cc_final: 0.8088 (m100) REVERT: B 258 ASP cc_start: 0.6500 (m-30) cc_final: 0.6026 (t0) REVERT: B 262 MET cc_start: 0.7580 (tpt) cc_final: 0.6568 (tpt) REVERT: R 17 THR cc_start: 0.8285 (p) cc_final: 0.8024 (t) REVERT: R 171 MET cc_start: 0.8121 (tpp) cc_final: 0.7559 (tpp) REVERT: R 206 ARG cc_start: 0.8378 (ttt90) cc_final: 0.8091 (tpt-90) REVERT: A 21 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8462 (ttm110) REVERT: A 28 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7770 (mm-30) REVERT: A 53 MET cc_start: 0.6121 (tpp) cc_final: 0.5598 (tpp) REVERT: A 204 GLN cc_start: 0.9300 (tp-100) cc_final: 0.9073 (tp-100) REVERT: A 287 TYR cc_start: 0.7436 (t80) cc_final: 0.7229 (t80) REVERT: A 293 SER cc_start: 0.9126 (t) cc_final: 0.8837 (p) REVERT: A 333 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8246 (tm-30) REVERT: A 337 ASP cc_start: 0.8459 (m-30) cc_final: 0.8126 (m-30) REVERT: A 354 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.5643 (m-80) REVERT: S 93 MET cc_start: 0.7822 (mmm) cc_final: 0.7576 (tmm) outliers start: 23 outliers final: 12 residues processed: 240 average time/residue: 0.2327 time to fit residues: 74.7465 Evaluate side-chains 186 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 18 MET 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: 8.9990 chunk 27 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.0570 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 91 HIS ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 95 HIS R 249 ASN A 304 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.128409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.104351 restraints weight = 22593.878| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 4.34 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8874 Z= 0.222 Angle : 0.666 10.071 12018 Z= 0.353 Chirality : 0.045 0.226 1376 Planarity : 0.005 0.049 1498 Dihedral : 4.710 54.581 1216 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 2.31 % Allowed : 17.00 % Favored : 80.69 % 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: 1.36 (0.28), residues: 364 sheet: -0.78 (0.29), residues: 285 loop : -0.46 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 184 HIS 0.006 0.001 HIS R 95 PHE 0.021 0.002 PHE R 93 TYR 0.015 0.001 TYR S 60 ARG 0.010 0.001 ARG A 205 *********************** 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 225 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.905 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 82 TRP cc_start: 0.8472 (m100) cc_final: 0.8083 (m100) REVERT: B 176 GLN cc_start: 0.8800 (pt0) cc_final: 0.8531 (pt0) REVERT: B 219 ARG cc_start: 0.7649 (ttt-90) cc_final: 0.7441 (mmm-85) REVERT: B 258 ASP cc_start: 0.7054 (m-30) cc_final: 0.6617 (t70) REVERT: R 17 THR cc_start: 0.8295 (p) cc_final: 0.8015 (t) REVERT: A 53 MET cc_start: 0.5785 (tpp) cc_final: 0.5132 (tpp) REVERT: A 287 TYR cc_start: 0.7460 (t80) cc_final: 0.7253 (t80) REVERT: A 354 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.5882 (m-80) REVERT: S 19 LYS cc_start: 0.8885 (mttm) cc_final: 0.8191 (mmtm) REVERT: S 34 MET cc_start: 0.6925 (mmp) cc_final: 0.5972 (mmp) REVERT: S 93 MET cc_start: 0.7897 (mmm) cc_final: 0.7684 (tmm) outliers start: 22 outliers final: 10 residues processed: 213 average time/residue: 0.2447 time to fit residues: 68.7132 Evaluate side-chains 173 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 174 GLN Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** R 44 GLN R 249 ASN A 244 HIS A 256 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.128664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.103307 restraints weight = 21882.487| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 4.46 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8874 Z= 0.202 Angle : 0.648 10.165 12018 Z= 0.338 Chirality : 0.043 0.156 1376 Planarity : 0.004 0.042 1498 Dihedral : 4.518 54.181 1216 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 3.36 % Allowed : 19.73 % Favored : 76.92 % 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: 0.16 (0.26), residues: 1085 helix: 1.52 (0.28), residues: 370 sheet: -0.63 (0.29), residues: 285 loop : -0.51 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP R 184 HIS 0.003 0.001 HIS R 271 PHE 0.027 0.002 PHE R 50 TYR 0.015 0.001 TYR S 94 ARG 0.005 0.001 ARG B 134 *********************** 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 215 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.941 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 82 TRP cc_start: 0.8518 (m100) cc_final: 0.8089 (m100) REVERT: B 176 GLN cc_start: 0.8857 (pt0) cc_final: 0.8632 (pt0) REVERT: B 258 ASP cc_start: 0.6903 (m-30) cc_final: 0.6460 (t0) REVERT: B 292 PHE cc_start: 0.8232 (m-80) cc_final: 0.7927 (m-80) REVERT: B 335 PHE cc_start: 0.7463 (m-10) cc_final: 0.7242 (m-10) REVERT: R 17 THR cc_start: 0.8345 (p) cc_final: 0.8094 (t) REVERT: A 44 SER cc_start: 0.7346 (t) cc_final: 0.6974 (p) REVERT: A 53 MET cc_start: 0.5530 (tpp) cc_final: 0.4916 (tpp) REVERT: A 354 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.5824 (m-80) REVERT: S 19 LYS cc_start: 0.8716 (mttm) cc_final: 0.8107 (mmtp) REVERT: S 34 MET cc_start: 0.7064 (mmp) cc_final: 0.6086 (mmp) REVERT: S 93 MET cc_start: 0.8113 (mmm) cc_final: 0.7871 (tmm) REVERT: S 94 TYR cc_start: 0.8291 (m-80) cc_final: 0.7857 (m-10) REVERT: S 103 TYR cc_start: 0.7544 (t80) cc_final: 0.7111 (t80) REVERT: S 234 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7728 (mp0) outliers start: 32 outliers final: 17 residues processed: 203 average time/residue: 0.2438 time to fit residues: 66.6890 Evaluate side-chains 174 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 281 TYR 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 331 ASN Chi-restraints excluded: chain A residue 354 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 295 ASN A 256 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.124600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.100845 restraints weight = 22403.369| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 4.25 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.6580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8874 Z= 0.243 Angle : 0.683 10.002 12018 Z= 0.352 Chirality : 0.043 0.164 1376 Planarity : 0.004 0.038 1498 Dihedral : 4.590 53.997 1216 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 3.57 % Allowed : 21.83 % Favored : 74.61 % 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: 0.15 (0.26), residues: 1085 helix: 1.43 (0.28), residues: 376 sheet: -0.60 (0.31), residues: 273 loop : -0.50 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 184 HIS 0.005 0.001 HIS B 225 PHE 0.020 0.002 PHE B 253 TYR 0.023 0.002 TYR S 178 ARG 0.004 0.001 ARG A 15 *********************** 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 213 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.848 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: 0.6834 (OUTLIER) cc_final: 0.6409 (tp) REVERT: B 124 TYR cc_start: 0.8158 (m-80) cc_final: 0.7936 (m-80) REVERT: B 258 ASP cc_start: 0.7007 (m-30) cc_final: 0.6435 (t0) REVERT: B 292 PHE cc_start: 0.8301 (m-80) cc_final: 0.7963 (m-80) REVERT: R 17 THR cc_start: 0.8373 (p) cc_final: 0.8128 (t) REVERT: R 30 ASN cc_start: 0.7235 (m-40) cc_final: 0.6934 (m-40) REVERT: R 58 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7651 (t70) REVERT: R 184 TRP cc_start: 0.7464 (m-90) cc_final: 0.6913 (m-90) REVERT: R 283 TYR cc_start: 0.8614 (t80) cc_final: 0.8392 (t80) REVERT: R 284 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8025 (mmmt) REVERT: A 44 SER cc_start: 0.7530 (t) cc_final: 0.7019 (t) REVERT: A 53 MET cc_start: 0.5783 (tpp) cc_final: 0.5169 (tpp) REVERT: A 205 ARG cc_start: 0.7994 (tmm160) cc_final: 0.7763 (ptt-90) REVERT: A 267 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8337 (m-80) REVERT: A 354 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: S 19 LYS cc_start: 0.8762 (mttm) cc_final: 0.8162 (mmtm) REVERT: S 103 TYR cc_start: 0.7641 (t80) cc_final: 0.7289 (t80) REVERT: G 47 GLU cc_start: 0.8057 (tp30) cc_final: 0.7775 (tp30) outliers start: 34 outliers final: 19 residues processed: 202 average time/residue: 0.2263 time to fit residues: 61.7023 Evaluate side-chains 176 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 B residue 336 LEU Chi-restraints excluded: chain R residue 34 ILE 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 267 PHE Chi-restraints excluded: chain A residue 331 ASN 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 174 GLN Chi-restraints excluded: chain S residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 106 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** S 130 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 = 0.4025 r_free = 0.4025 target = 0.123699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.099890 restraints weight = 22610.978| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 4.31 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8874 Z= 0.219 Angle : 0.680 10.385 12018 Z= 0.350 Chirality : 0.044 0.207 1376 Planarity : 0.004 0.036 1498 Dihedral : 4.494 53.929 1216 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 3.46 % Allowed : 23.40 % Favored : 73.14 % 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: 1.65 (0.28), residues: 370 sheet: -0.62 (0.30), residues: 273 loop : -0.44 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.026 0.002 PHE R 50 TYR 0.021 0.001 TYR S 178 ARG 0.008 0.001 ARG A 208 *********************** 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 211 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.977 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: 0.6842 (OUTLIER) cc_final: 0.6419 (tp) REVERT: B 124 TYR cc_start: 0.8117 (m-80) cc_final: 0.7870 (m-80) REVERT: B 226 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7938 (mp0) REVERT: B 292 PHE cc_start: 0.8280 (m-80) cc_final: 0.7848 (m-80) REVERT: R 17 THR cc_start: 0.8309 (p) cc_final: 0.8056 (t) REVERT: R 58 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7773 (t70) REVERT: R 173 MET cc_start: 0.7470 (mmm) cc_final: 0.7248 (mpp) REVERT: R 184 TRP cc_start: 0.7426 (m-90) cc_final: 0.6750 (m-90) REVERT: R 283 TYR cc_start: 0.8574 (t80) cc_final: 0.8354 (t80) REVERT: A 44 SER cc_start: 0.7587 (t) cc_final: 0.7092 (t) REVERT: A 53 MET cc_start: 0.5679 (tpp) cc_final: 0.5042 (tpp) REVERT: A 205 ARG cc_start: 0.7972 (tmm160) cc_final: 0.7729 (ptt-90) REVERT: A 354 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6068 (m-80) REVERT: S 19 LYS cc_start: 0.8794 (mttm) cc_final: 0.8121 (mmtp) REVERT: S 43 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8681 (mmmm) REVERT: S 103 TYR cc_start: 0.7597 (t80) cc_final: 0.7373 (t80) REVERT: G 47 GLU cc_start: 0.8145 (tp30) cc_final: 0.7901 (tp30) outliers start: 33 outliers final: 17 residues processed: 201 average time/residue: 0.2227 time to fit residues: 60.7726 Evaluate side-chains 174 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 58 ASP Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 98 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 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 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: 6.9990 chunk 19 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 205 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.125025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.100435 restraints weight = 22584.403| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 4.42 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.7295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8874 Z= 0.201 Angle : 0.692 10.506 12018 Z= 0.355 Chirality : 0.043 0.166 1376 Planarity : 0.004 0.035 1498 Dihedral : 4.522 53.243 1216 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 3.04 % Allowed : 24.24 % Favored : 72.72 % 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: 0.27 (0.26), residues: 1085 helix: 1.54 (0.28), residues: 377 sheet: -0.47 (0.31), residues: 268 loop : -0.49 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.001 PHE B 253 TYR 0.014 0.001 TYR S 94 ARG 0.007 0.000 ARG R 206 *********************** 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 199 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.038 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: 0.6867 (OUTLIER) cc_final: 0.6416 (tp) REVERT: B 124 TYR cc_start: 0.7951 (m-80) cc_final: 0.7708 (m-80) REVERT: B 133 VAL cc_start: 0.8101 (t) cc_final: 0.7876 (m) REVERT: B 226 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7950 (mp0) REVERT: B 280 LYS cc_start: 0.8499 (tttm) cc_final: 0.7751 (tttt) REVERT: B 292 PHE cc_start: 0.8204 (m-80) cc_final: 0.7719 (m-80) REVERT: B 297 TRP cc_start: 0.7660 (m100) cc_final: 0.7355 (m100) REVERT: R 15 TYR cc_start: 0.7142 (t80) cc_final: 0.6841 (t80) REVERT: R 58 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8208 (t70) REVERT: R 119 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8227 (mmm-85) REVERT: R 183 LEU cc_start: 0.8121 (tp) cc_final: 0.7760 (tp) REVERT: R 283 TYR cc_start: 0.8549 (t80) cc_final: 0.8334 (t80) REVERT: A 44 SER cc_start: 0.7581 (t) cc_final: 0.7119 (t) REVERT: A 53 MET cc_start: 0.5714 (tpp) cc_final: 0.5086 (tpp) REVERT: A 205 ARG cc_start: 0.8016 (tmm160) cc_final: 0.7779 (ptt-90) REVERT: A 354 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6056 (m-80) REVERT: S 19 LYS cc_start: 0.8699 (mttm) cc_final: 0.8149 (mmtm) REVERT: G 44 HIS cc_start: 0.7913 (m90) cc_final: 0.7116 (t70) REVERT: G 47 GLU cc_start: 0.8344 (tp30) cc_final: 0.7428 (tp30) outliers start: 29 outliers final: 19 residues processed: 190 average time/residue: 0.2283 time to fit residues: 58.3159 Evaluate side-chains 176 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 B residue 336 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 233 LEU Chi-restraints excluded: chain R residue 240 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 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 Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 60.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 293 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.122160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.097491 restraints weight = 22631.731| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 4.44 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.7699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8874 Z= 0.252 Angle : 0.706 10.963 12018 Z= 0.367 Chirality : 0.044 0.183 1376 Planarity : 0.004 0.035 1498 Dihedral : 4.682 53.836 1216 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 3.25 % Allowed : 24.45 % Favored : 72.30 % 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: 0.23 (0.26), residues: 1085 helix: 1.44 (0.27), residues: 375 sheet: -0.37 (0.31), residues: 272 loop : -0.52 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.006 0.001 HIS A 322 PHE 0.025 0.002 PHE R 50 TYR 0.024 0.002 TYR S 178 ARG 0.006 0.001 ARG R 206 *********************** 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 190 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.071 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: B 7 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6427 (tp) REVERT: B 82 TRP cc_start: 0.8571 (m100) cc_final: 0.8233 (m100) REVERT: B 292 PHE cc_start: 0.8375 (m-80) cc_final: 0.7714 (m-10) REVERT: B 297 TRP cc_start: 0.7759 (m100) cc_final: 0.7434 (m100) REVERT: R 15 TYR cc_start: 0.7274 (t80) cc_final: 0.6951 (t80) REVERT: R 58 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8084 (t70) REVERT: R 99 MET cc_start: 0.8783 (mmm) cc_final: 0.8558 (mmp) REVERT: R 113 LYS cc_start: 0.8064 (tmtt) cc_final: 0.7590 (tptp) REVERT: R 283 TYR cc_start: 0.8559 (t80) cc_final: 0.8317 (t80) REVERT: R 284 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8160 (mmmt) REVERT: A 33 GLU cc_start: 0.6927 (pp20) cc_final: 0.6415 (pp20) REVERT: A 44 SER cc_start: 0.7743 (t) cc_final: 0.7346 (t) REVERT: A 208 ARG cc_start: 0.7889 (tpp-160) cc_final: 0.7428 (tpp-160) REVERT: A 267 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8687 (m-80) REVERT: A 354 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6100 (m-80) REVERT: S 34 MET cc_start: 0.6487 (mmm) cc_final: 0.5724 (mmm) REVERT: S 207 LEU cc_start: 0.9116 (tt) cc_final: 0.8788 (pt) REVERT: S 234 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8315 (mp0) REVERT: G 47 GLU cc_start: 0.8400 (tp30) cc_final: 0.7903 (tp30) outliers start: 31 outliers final: 23 residues processed: 179 average time/residue: 0.2317 time to fit residues: 55.8669 Evaluate side-chains 178 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 B residue 336 LEU Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 58 ASP Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 98 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 202 ILE Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 240 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 267 PHE Chi-restraints excluded: chain A residue 331 ASN 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 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: 2.9990 chunk 87 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 107 optimal weight: 0.0000 chunk 31 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** S 130 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 = 0.4024 r_free = 0.4024 target = 0.124393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.099771 restraints weight = 22648.235| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 4.47 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.7943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8874 Z= 0.212 Angle : 0.713 11.777 12018 Z= 0.366 Chirality : 0.043 0.230 1376 Planarity : 0.004 0.035 1498 Dihedral : 4.725 53.046 1216 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 2.94 % Allowed : 25.81 % Favored : 71.25 % 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: 0.23 (0.26), residues: 1085 helix: 1.45 (0.27), residues: 378 sheet: -0.37 (0.31), residues: 267 loop : -0.56 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 164 HIS 0.003 0.001 HIS B 183 PHE 0.050 0.002 PHE R 93 TYR 0.023 0.002 TYR S 178 ARG 0.006 0.001 ARG R 206 *********************** 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 : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6408 (tp) REVERT: B 82 TRP cc_start: 0.8506 (m100) cc_final: 0.8299 (m100) REVERT: B 226 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8043 (mp0) REVERT: B 262 MET cc_start: 0.7407 (mmm) cc_final: 0.7012 (mmt) REVERT: B 292 PHE cc_start: 0.8321 (m-80) cc_final: 0.7794 (m-80) REVERT: B 297 TRP cc_start: 0.7674 (m100) cc_final: 0.7193 (m100) REVERT: R 58 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8229 (t70) REVERT: R 90 MET cc_start: 0.6216 (mmt) cc_final: 0.5557 (mmt) REVERT: R 93 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6695 (t80) REVERT: R 99 MET cc_start: 0.8809 (mmm) cc_final: 0.8573 (mmp) REVERT: R 113 LYS cc_start: 0.7796 (tmtt) cc_final: 0.7335 (tptp) REVERT: R 275 MET cc_start: 0.7900 (tmm) cc_final: 0.7165 (tpt) REVERT: R 283 TYR cc_start: 0.8541 (t80) cc_final: 0.8312 (t80) REVERT: R 284 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8215 (mmmt) REVERT: R 290 GLU cc_start: 0.8658 (mp0) cc_final: 0.8239 (mp0) REVERT: A 33 GLU cc_start: 0.6816 (pp20) cc_final: 0.6525 (pp20) REVERT: A 44 SER cc_start: 0.7461 (t) cc_final: 0.7080 (t) REVERT: A 195 HIS cc_start: 0.8200 (t-90) cc_final: 0.7907 (t-90) REVERT: A 208 ARG cc_start: 0.7839 (tpp-160) cc_final: 0.7447 (tpp-160) REVERT: A 354 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6218 (m-80) REVERT: S 19 LYS cc_start: 0.8670 (mttm) cc_final: 0.8165 (mmmm) REVERT: S 34 MET cc_start: 0.6423 (mmm) cc_final: 0.5721 (mmm) REVERT: S 234 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8414 (mp0) REVERT: G 47 GLU cc_start: 0.8296 (tp30) cc_final: 0.7741 (tp30) outliers start: 28 outliers final: 20 residues processed: 188 average time/residue: 0.2251 time to fit residues: 57.4406 Evaluate side-chains 176 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 58 ASP Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 98 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 233 LEU Chi-restraints excluded: chain R residue 240 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 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: 5.9990 chunk 88 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 103 optimal weight: 0.0970 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 0.0020 chunk 2 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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** ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 249 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.126033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.101771 restraints weight = 22484.967| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 4.42 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.8088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8874 Z= 0.197 Angle : 0.723 13.441 12018 Z= 0.367 Chirality : 0.044 0.195 1376 Planarity : 0.004 0.035 1498 Dihedral : 4.670 51.200 1216 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.52 % Allowed : 26.65 % Favored : 70.83 % 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: 0.34 (0.26), residues: 1085 helix: 1.55 (0.27), residues: 379 sheet: -0.39 (0.31), residues: 276 loop : -0.43 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 164 HIS 0.004 0.001 HIS A 322 PHE 0.034 0.002 PHE R 93 TYR 0.023 0.001 TYR S 178 ARG 0.009 0.001 ARG S 206 ********************** 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: 24 poor density : 166 time to evaluate : 1.041 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: 0.6883 (OUTLIER) cc_final: 0.6434 (tp) REVERT: B 138 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7427 (mt-10) REVERT: B 226 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8125 (mp0) REVERT: B 262 MET cc_start: 0.7444 (mmm) cc_final: 0.7056 (mmt) REVERT: B 280 LYS cc_start: 0.8581 (tttm) cc_final: 0.7855 (tttm) REVERT: B 297 TRP cc_start: 0.7717 (m100) cc_final: 0.7226 (m100) REVERT: R 15 TYR cc_start: 0.6855 (t80) cc_final: 0.6485 (t80) REVERT: R 58 ASP cc_start: 0.8636 (t0) cc_final: 0.8421 (t70) REVERT: R 90 MET cc_start: 0.6235 (mmt) cc_final: 0.5707 (mmt) REVERT: R 93 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6526 (t80) REVERT: R 99 MET cc_start: 0.8786 (mmm) cc_final: 0.8550 (mmp) REVERT: R 113 LYS cc_start: 0.7756 (tmtt) cc_final: 0.7331 (tptp) REVERT: R 275 MET cc_start: 0.7852 (tmm) cc_final: 0.7200 (tpt) REVERT: R 283 TYR cc_start: 0.8528 (t80) cc_final: 0.8304 (t80) REVERT: R 284 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8118 (mmmt) REVERT: R 290 GLU cc_start: 0.8594 (mp0) cc_final: 0.8202 (mp0) REVERT: A 44 SER cc_start: 0.7525 (t) cc_final: 0.7148 (t) REVERT: A 195 HIS cc_start: 0.8118 (t-90) cc_final: 0.7827 (t-90) REVERT: A 208 ARG cc_start: 0.7975 (tpp-160) cc_final: 0.7497 (tpp-160) REVERT: A 354 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: S 34 MET cc_start: 0.6402 (mmm) cc_final: 0.5745 (mmm) REVERT: S 207 LEU cc_start: 0.9298 (tt) cc_final: 0.9054 (pt) REVERT: G 44 HIS cc_start: 0.8031 (m90) cc_final: 0.7097 (t70) REVERT: G 47 GLU cc_start: 0.8158 (tp30) cc_final: 0.7560 (tp30) outliers start: 24 outliers final: 19 residues processed: 184 average time/residue: 0.2265 time to fit residues: 56.0793 Evaluate side-chains 177 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 83 CYS Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 98 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 18 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 331 ASN 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: 1.9990 chunk 79 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 340 ASN ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 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 = 0.4037 r_free = 0.4037 target = 0.124910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100511 restraints weight = 22503.480| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 4.42 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.8219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8874 Z= 0.218 Angle : 0.742 12.718 12018 Z= 0.375 Chirality : 0.044 0.233 1376 Planarity : 0.004 0.035 1498 Dihedral : 4.721 50.687 1216 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.52 % Allowed : 27.18 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.32 (0.26), residues: 1085 helix: 1.52 (0.27), residues: 379 sheet: -0.40 (0.31), residues: 276 loop : -0.44 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 82 HIS 0.003 0.001 HIS A 322 PHE 0.036 0.002 PHE R 93 TYR 0.022 0.001 TYR S 178 ARG 0.009 0.001 ARG R 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4236.50 seconds wall clock time: 76 minutes 32.52 seconds (4592.52 seconds total)