Starting phenix.real_space_refine on Thu Jul 2 13:32:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ljc_23390/07_2026/7ljc_23390.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ljc_23390/07_2026/7ljc_23390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ljc_23390/07_2026/7ljc_23390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ljc_23390/07_2026/7ljc_23390.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ljc_23390/07_2026/7ljc_23390.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ljc_23390/07_2026/7ljc_23390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ljc_23390/07_2026/7ljc_23390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ljc_23390/07_2026/7ljc_23390.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.037 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: 5 Type Number sf(0) Gaussians S 55 5.16 5 Cl 3 4.86 5 C 5505 2.51 5 N 1442 2.21 5 O 1539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8544 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2226 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 3 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1989 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 326 Unusual residues: {'CLR': 6, 'G4C': 1, 'PLM': 6, 'SK0': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Time building chain proxies: 1.76, per 1000 atoms: 0.21 Number of scatterers: 8544 At special positions: 0 Unit cell: (91.96, 108.68, 123.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 3 17.00 S 55 16.00 O 1539 8.00 N 1442 7.00 C 5505 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 0.53 Conformation dependent library (CDL) restraints added in 382.5 milliseconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.9% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'R' and resid 21 through 51 Processing helix chain 'R' and resid 51 through 56 removed outlier: 4.122A pdb=" N ARG R 55 " --> pdb=" O PHE R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 removed outlier: 4.057A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL R 77 " --> pdb=" O VAL R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 Processing helix chain 'R' and resid 94 through 127 removed outlier: 4.339A pdb=" N ILE R 98 " --> pdb=" O SER R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 161 removed outlier: 4.294A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 191 through 203 Processing helix chain 'R' and resid 203 through 240 Processing helix chain 'R' and resid 265 through 298 removed outlier: 3.696A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 309 through 332 removed outlier: 3.975A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'A' and resid 10 through 40 Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.500A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.621A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.985A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 205 removed outlier: 3.829A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.618A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.579A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 5.959A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.803A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.926A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.263A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.533A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.809A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.225A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.763A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.926A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1302 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: 1.10 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2148 1.33 - 1.46: 1881 1.46 - 1.58: 4623 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8730 Sorted by residual: bond pdb=" C05 G4C R 502 " pdb=" N04 G4C R 502 " ideal model delta sigma weight residual 1.355 1.498 -0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.02e+00 bond pdb=" C ASN R 327 " pdb=" N PRO R 328 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.64e+00 bond pdb=" C MET R 78 " pdb=" N PRO R 79 " ideal model delta sigma weight residual 1.335 1.360 -0.024 1.36e-02 5.41e+03 3.21e+00 bond pdb=" C LEU R 286 " pdb=" N PRO R 287 " ideal model delta sigma weight residual 1.335 1.360 -0.024 1.36e-02 5.41e+03 3.18e+00 ... (remaining 8725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 11092 1.90 - 3.81: 619 3.81 - 5.71: 77 5.71 - 7.61: 34 7.61 - 9.52: 7 Bond angle restraints: 11829 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" N GLY B 244 " pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 113.18 105.26 7.92 2.37e+00 1.78e-01 1.12e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 115.81 -3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" N SER B 275 " pdb=" CA SER B 275 " pdb=" C SER B 275 " ideal model delta sigma weight residual 109.06 114.24 -5.18 1.70e+00 3.46e-01 9.28e+00 ... (remaining 11824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5020 17.55 - 35.09: 114 35.09 - 52.64: 20 52.64 - 70.18: 2 70.18 - 87.73: 2 Dihedral angle restraints: 5158 sinusoidal: 2122 harmonic: 3036 Sorted by residual: dihedral pdb=" CA GLY B 53 " pdb=" C GLY B 53 " pdb=" N HIS B 54 " pdb=" CA HIS B 54 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1158 0.091 - 0.183: 149 0.183 - 0.274: 12 0.274 - 0.366: 6 0.366 - 0.457: 6 Chirality restraints: 1331 Sorted by residual: chirality pdb=" C14 CLR R 508 " pdb=" C13 CLR R 508 " pdb=" C15 CLR R 508 " pdb=" C8 CLR R 508 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C14 CLR R 507 " pdb=" C13 CLR R 507 " pdb=" C15 CLR R 507 " pdb=" C8 CLR R 507 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.23e+00 ... (remaining 1328 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 G4C R 502 " 0.225 2.00e-02 2.50e+03 1.56e-01 3.67e+02 pdb=" C05 G4C R 502 " -0.051 2.00e-02 2.50e+03 pdb=" C06 G4C R 502 " 0.180 2.00e-02 2.50e+03 pdb=" C16 G4C R 502 " -0.036 2.00e-02 2.50e+03 pdb=" N04 G4C R 502 " -0.227 2.00e-02 2.50e+03 pdb=" O15 G4C R 502 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 101 " -0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C ALA R 101 " 0.073 2.00e-02 2.50e+03 pdb=" O ALA R 101 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE R 102 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 110 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER R 110 " -0.068 2.00e-02 2.50e+03 pdb=" O SER R 110 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE R 111 " 0.023 2.00e-02 2.50e+03 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2090 2.81 - 3.33: 7663 3.33 - 3.85: 14340 3.85 - 4.38: 16516 4.38 - 4.90: 28840 Nonbonded interactions: 69449 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 170 " pdb=" OD2 ASP A 195 " model vdw 2.288 3.040 nonbonded pdb=" OG SER R 198 " pdb=" O02 SK0 R 501 " model vdw 2.335 3.040 nonbonded pdb=" OG1 THR R 59 " pdb=" OH TYR R 131 " model vdw 2.371 3.040 nonbonded pdb=" NH2 ARG R 133 " pdb=" O LYS A 78 " model vdw 2.371 3.120 ... (remaining 69444 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: 0.370 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 8.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.005 0.143 8734 Z= 0.266 Angle : 1.006 9.518 11837 Z= 0.545 Chirality : 0.068 0.457 1331 Planarity : 0.009 0.156 1458 Dihedral : 8.580 87.728 3174 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.11 % Allowed : 0.34 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.23), residues: 1024 helix: 0.47 (0.21), residues: 389 sheet: -0.65 (0.32), residues: 239 loop : -1.87 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 194 TYR 0.022 0.002 TYR N 95 PHE 0.030 0.003 PHE B 278 TRP 0.032 0.003 TRP A 133 HIS 0.009 0.003 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.27 ( 8730) covalent geometry : angle 1.00461 / 0.54 (11829) SS BOND : bond 0.00217 / 0.11 ( 4) SS BOND : angle 2.34681 / 1.43 ( 8) hydrogen bonds : bond 0.14021 / 9.32 ( 452) hydrogen bonds : angle 6.83760 / 5.00 ( 1302) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: R 76 LEU cc_start: 0.7934 (mp) cc_final: 0.7726 (mt) REVERT: R 126 SER cc_start: 0.8928 (t) cc_final: 0.8707 (p) REVERT: R 127 SER cc_start: 0.8729 (m) cc_final: 0.8474 (p) REVERT: R 154 ILE cc_start: 0.7667 (mt) cc_final: 0.7186 (tt) REVERT: R 270 VAL cc_start: 0.8186 (t) cc_final: 0.7877 (p) REVERT: A 24 LYS cc_start: 0.8585 (mmmt) cc_final: 0.8318 (mmmt) REVERT: A 60 MET cc_start: 0.6708 (ttt) cc_final: 0.6372 (ttt) REVERT: A 75 GLN cc_start: 0.7846 (tt0) cc_final: 0.7549 (tt0) REVERT: A 142 PHE cc_start: 0.8762 (m-80) cc_final: 0.8437 (m-80) REVERT: A 169 ARG cc_start: 0.8271 (ptp-170) cc_final: 0.7918 (ptp-170) REVERT: A 202 THR cc_start: 0.8451 (m) cc_final: 0.8029 (p) REVERT: A 208 ARG cc_start: 0.8559 (mtm180) cc_final: 0.8299 (mtm180) REVERT: A 229 ASN cc_start: 0.8659 (m-40) cc_final: 0.8265 (m-40) REVERT: A 233 ASP cc_start: 0.8578 (m-30) cc_final: 0.8364 (m-30) REVERT: A 244 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8211 (mt-10) REVERT: B 14 LEU cc_start: 0.8487 (mt) cc_final: 0.8282 (mt) REVERT: B 25 CYS cc_start: 0.8473 (m) cc_final: 0.8114 (p) REVERT: B 52 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8177 (mtt-85) REVERT: B 98 SER cc_start: 0.8371 (m) cc_final: 0.7982 (p) REVERT: B 111 TYR cc_start: 0.8228 (m-80) cc_final: 0.7865 (m-80) REVERT: B 195 ASP cc_start: 0.7961 (p0) cc_final: 0.7747 (p0) REVERT: B 197 ARG cc_start: 0.7941 (mmt180) cc_final: 0.7580 (mmt180) REVERT: B 239 ASN cc_start: 0.8115 (m-40) cc_final: 0.7769 (m-40) REVERT: B 247 ASP cc_start: 0.7841 (p0) cc_final: 0.7555 (p0) REVERT: B 254 ASP cc_start: 0.8653 (t0) cc_final: 0.8419 (t70) REVERT: B 258 ASP cc_start: 0.8091 (t0) cc_final: 0.7374 (t0) REVERT: B 262 MET cc_start: 0.8576 (ttm) cc_final: 0.8307 (ttm) REVERT: B 264 TYR cc_start: 0.8593 (m-80) cc_final: 0.8102 (m-80) REVERT: B 273 ILE cc_start: 0.8118 (mt) cc_final: 0.7872 (mt) REVERT: B 289 TYR cc_start: 0.8516 (m-80) cc_final: 0.8242 (m-80) REVERT: B 312 ASP cc_start: 0.8630 (t0) cc_final: 0.8363 (t0) REVERT: N 112 SER cc_start: 0.8084 (p) cc_final: 0.7724 (m) outliers start: 1 outliers final: 3 residues processed: 294 average time/residue: 0.4109 time to fit residues: 129.4363 Evaluate side-chains 256 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 253 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 198 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 41 ASN R 164 HIS R 222 GLN A 19 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS B 62 HIS B 88 ASN B 91 HIS B 259 GLN N 5 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.143752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127495 restraints weight = 11621.029| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.03 r_work: 0.3510 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8734 Z= 0.147 Angle : 0.572 16.246 11837 Z= 0.295 Chirality : 0.041 0.215 1331 Planarity : 0.005 0.047 1458 Dihedral : 5.985 86.182 1283 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.91 % Allowed : 10.95 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1024 helix: 2.30 (0.23), residues: 409 sheet: -0.39 (0.34), residues: 214 loop : -1.22 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 49 TYR 0.013 0.001 TYR B 124 PHE 0.021 0.002 PHE B 199 TRP 0.019 0.002 TRP B 82 HIS 0.009 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 8730) covalent geometry : angle 0.57140 / 0.30 (11829) SS BOND : bond 0.00137 / 0.07 ( 4) SS BOND : angle 0.88958 / 0.48 ( 8) hydrogen bonds : bond 0.04638 / 3.13 ( 452) hydrogen bonds : angle 5.11431 / 3.74 ( 1302) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: R 153 LEU cc_start: 0.8078 (mt) cc_final: 0.7843 (mt) REVERT: R 270 VAL cc_start: 0.7844 (t) cc_final: 0.7547 (p) REVERT: R 331 TYR cc_start: 0.8025 (m-80) cc_final: 0.7750 (m-80) REVERT: A 24 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7669 (tppp) REVERT: A 27 GLU cc_start: 0.7400 (tp30) cc_final: 0.7144 (tp30) REVERT: A 60 MET cc_start: 0.6107 (ttt) cc_final: 0.5795 (ttt) REVERT: A 70 PHE cc_start: 0.7804 (m-80) cc_final: 0.7588 (m-10) REVERT: A 75 GLN cc_start: 0.7321 (tt0) cc_final: 0.6846 (tt0) REVERT: A 77 ASP cc_start: 0.7657 (m-30) cc_final: 0.7328 (m-30) REVERT: A 93 ARG cc_start: 0.8455 (ptt90) cc_final: 0.8176 (ptp90) REVERT: A 111 ASP cc_start: 0.7854 (t0) cc_final: 0.7096 (t0) REVERT: A 114 ASP cc_start: 0.7597 (m-30) cc_final: 0.6824 (m-30) REVERT: A 142 PHE cc_start: 0.8491 (m-80) cc_final: 0.8262 (m-80) REVERT: A 151 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 169 ARG cc_start: 0.7968 (ptp-170) cc_final: 0.7556 (ptp-170) REVERT: A 200 ILE cc_start: 0.8447 (mt) cc_final: 0.8238 (mm) REVERT: A 202 THR cc_start: 0.8008 (m) cc_final: 0.7584 (p) REVERT: A 208 ARG cc_start: 0.8179 (mtm180) cc_final: 0.7857 (mtm180) REVERT: A 229 ASN cc_start: 0.8275 (m-40) cc_final: 0.7748 (m-40) REVERT: A 233 ASP cc_start: 0.7726 (m-30) cc_final: 0.7376 (m-30) REVERT: A 244 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7592 (mt-10) REVERT: B 52 ARG cc_start: 0.7687 (mtt-85) cc_final: 0.7433 (mtt-85) REVERT: B 70 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8070 (pt) REVERT: B 98 SER cc_start: 0.8074 (m) cc_final: 0.7576 (p) REVERT: B 114 CYS cc_start: 0.7731 (p) cc_final: 0.7393 (p) REVERT: B 124 TYR cc_start: 0.8449 (m-80) cc_final: 0.8124 (m-80) REVERT: B 137 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.6932 (mmm-85) REVERT: B 158 VAL cc_start: 0.7784 (t) cc_final: 0.7552 (p) REVERT: B 186 ASP cc_start: 0.7831 (m-30) cc_final: 0.7560 (m-30) REVERT: B 195 ASP cc_start: 0.7691 (p0) cc_final: 0.7461 (p0) REVERT: B 197 ARG cc_start: 0.7619 (mmt180) cc_final: 0.7391 (mmt180) REVERT: B 221 THR cc_start: 0.8205 (m) cc_final: 0.7898 (t) REVERT: B 226 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 239 ASN cc_start: 0.7772 (m-40) cc_final: 0.7410 (m-40) REVERT: B 254 ASP cc_start: 0.7617 (t0) cc_final: 0.7155 (t70) REVERT: B 256 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7691 (mtt90) REVERT: B 258 ASP cc_start: 0.7338 (t0) cc_final: 0.6886 (t0) REVERT: B 277 SER cc_start: 0.8644 (t) cc_final: 0.8408 (t) REVERT: B 289 TYR cc_start: 0.8432 (m-80) cc_final: 0.8157 (m-80) REVERT: B 312 ASP cc_start: 0.7720 (t0) cc_final: 0.7408 (t0) REVERT: B 316 SER cc_start: 0.8045 (t) cc_final: 0.7820 (p) REVERT: N 112 SER cc_start: 0.8031 (p) cc_final: 0.7703 (m) outliers start: 26 outliers final: 10 residues processed: 268 average time/residue: 0.4352 time to fit residues: 124.6582 Evaluate side-chains 257 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 246 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 10 optimal weight: 0.0020 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 327 ASN A 75 GLN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 88 ASN B 110 ASN B 220 GLN B 259 GLN B 295 ASN N 5 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126922 restraints weight = 11457.308| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.00 r_work: 0.3506 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8734 Z= 0.124 Angle : 0.540 17.907 11837 Z= 0.273 Chirality : 0.040 0.144 1331 Planarity : 0.004 0.046 1458 Dihedral : 5.551 83.663 1281 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.35 % Allowed : 13.74 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.26), residues: 1024 helix: 2.72 (0.24), residues: 413 sheet: -0.20 (0.34), residues: 213 loop : -1.06 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 241 TYR 0.016 0.001 TYR B 105 PHE 0.017 0.001 PHE B 199 TRP 0.016 0.001 TRP A 133 HIS 0.006 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8730) covalent geometry : angle 0.53958 / 0.27 (11829) SS BOND : bond 0.00094 / 0.05 ( 4) SS BOND : angle 0.58448 / 0.33 ( 8) hydrogen bonds : bond 0.04276 / 2.89 ( 452) hydrogen bonds : angle 4.88978 / 3.58 ( 1302) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 49 ILE cc_start: 0.8104 (mm) cc_final: 0.7869 (mm) REVERT: R 153 LEU cc_start: 0.8012 (mt) cc_final: 0.7791 (mt) REVERT: R 154 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7050 (tt) REVERT: R 159 VAL cc_start: 0.7947 (t) cc_final: 0.7579 (m) REVERT: R 270 VAL cc_start: 0.7821 (t) cc_final: 0.7513 (p) REVERT: R 331 TYR cc_start: 0.8124 (m-80) cc_final: 0.7884 (m-80) REVERT: A 24 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7589 (tppp) REVERT: A 27 GLU cc_start: 0.7378 (tp30) cc_final: 0.7130 (tp30) REVERT: A 36 VAL cc_start: 0.8343 (p) cc_final: 0.8126 (t) REVERT: A 70 PHE cc_start: 0.7764 (m-80) cc_final: 0.7562 (m-10) REVERT: A 77 ASP cc_start: 0.7637 (m-30) cc_final: 0.7286 (m-30) REVERT: A 93 ARG cc_start: 0.8435 (ptt90) cc_final: 0.8167 (ptp90) REVERT: A 111 ASP cc_start: 0.7843 (t0) cc_final: 0.7588 (t0) REVERT: A 117 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7910 (mtp180) REVERT: A 130 ASN cc_start: 0.8540 (m-40) cc_final: 0.8282 (m110) REVERT: A 142 PHE cc_start: 0.8430 (m-80) cc_final: 0.8220 (m-80) REVERT: A 169 ARG cc_start: 0.7951 (ptp-170) cc_final: 0.7575 (mtm-85) REVERT: A 202 THR cc_start: 0.7982 (m) cc_final: 0.7559 (p) REVERT: A 208 ARG cc_start: 0.8244 (mtm180) cc_final: 0.7924 (mtm180) REVERT: A 229 ASN cc_start: 0.8298 (m-40) cc_final: 0.7784 (m-40) REVERT: A 233 ASP cc_start: 0.7734 (m-30) cc_final: 0.7399 (m-30) REVERT: A 244 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7573 (mt-10) REVERT: B 25 CYS cc_start: 0.8134 (m) cc_final: 0.7500 (p) REVERT: B 52 ARG cc_start: 0.7687 (mtt-85) cc_final: 0.7450 (mtt-85) REVERT: B 83 ASP cc_start: 0.8289 (t0) cc_final: 0.8011 (t70) REVERT: B 98 SER cc_start: 0.8047 (m) cc_final: 0.7586 (p) REVERT: B 114 CYS cc_start: 0.7720 (p) cc_final: 0.7435 (p) REVERT: B 124 TYR cc_start: 0.8478 (m-80) cc_final: 0.8193 (m-80) REVERT: B 137 ARG cc_start: 0.7521 (ttm-80) cc_final: 0.6974 (mmm-85) REVERT: B 163 ASP cc_start: 0.7523 (p0) cc_final: 0.7318 (p0) REVERT: B 197 ARG cc_start: 0.7620 (mmt180) cc_final: 0.7389 (mmt180) REVERT: B 221 THR cc_start: 0.8227 (m) cc_final: 0.7943 (t) REVERT: B 226 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 239 ASN cc_start: 0.7683 (m-40) cc_final: 0.7259 (m-40) REVERT: B 256 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7635 (mtt90) REVERT: B 258 ASP cc_start: 0.7451 (t0) cc_final: 0.7029 (t0) REVERT: B 259 GLN cc_start: 0.8342 (pt0) cc_final: 0.7898 (pt0) REVERT: B 277 SER cc_start: 0.8573 (t) cc_final: 0.8248 (p) REVERT: B 312 ASP cc_start: 0.7737 (t0) cc_final: 0.7318 (t0) REVERT: N 112 SER cc_start: 0.8021 (p) cc_final: 0.7817 (m) outliers start: 21 outliers final: 11 residues processed: 251 average time/residue: 0.4519 time to fit residues: 120.7830 Evaluate side-chains 240 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 327 ASN A 29 GLN A 75 GLN A 123 ASN A 236 GLN B 88 ASN B 220 GLN ** N 35 ASN ** 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 = 0.3784 r_free = 0.3784 target = 0.141135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124955 restraints weight = 11609.059| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.97 r_work: 0.3405 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8734 Z= 0.217 Angle : 0.581 17.877 11837 Z= 0.295 Chirality : 0.042 0.152 1331 Planarity : 0.005 0.055 1458 Dihedral : 5.839 84.798 1281 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.57 % Allowed : 13.97 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1024 helix: 2.41 (0.24), residues: 418 sheet: -0.54 (0.33), residues: 208 loop : -0.85 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 241 TYR 0.021 0.002 TYR N 117 PHE 0.018 0.002 PHE N 68 TRP 0.022 0.002 TRP A 133 HIS 0.007 0.002 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 ( 8730) covalent geometry : angle 0.58017 / 0.29 (11829) SS BOND : bond 0.00319 / 0.16 ( 4) SS BOND : angle 1.20031 / 0.72 ( 8) hydrogen bonds : bond 0.04582 / 3.11 ( 452) hydrogen bonds : angle 5.07283 / 3.70 ( 1302) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8248 (mtt) REVERT: R 153 LEU cc_start: 0.8005 (mt) cc_final: 0.7797 (mt) REVERT: R 154 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7411 (mp) REVERT: R 159 VAL cc_start: 0.7915 (t) cc_final: 0.7553 (m) REVERT: R 270 VAL cc_start: 0.8006 (t) cc_final: 0.7658 (p) REVERT: R 298 CYS cc_start: 0.6539 (t) cc_final: 0.6285 (t) REVERT: R 331 TYR cc_start: 0.8375 (m-80) cc_final: 0.8108 (m-80) REVERT: A 24 LYS cc_start: 0.7884 (mmmt) cc_final: 0.7660 (mmmt) REVERT: A 60 MET cc_start: 0.5856 (ttt) cc_final: 0.5581 (ttt) REVERT: A 75 GLN cc_start: 0.7787 (tt0) cc_final: 0.7336 (tt0) REVERT: A 77 ASP cc_start: 0.7771 (m-30) cc_final: 0.7352 (m-30) REVERT: A 89 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7480 (mm-40) REVERT: A 93 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8069 (ptt180) REVERT: A 111 ASP cc_start: 0.7880 (t0) cc_final: 0.7520 (t0) REVERT: A 151 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7537 (mt-10) REVERT: A 169 ARG cc_start: 0.8005 (ptp-170) cc_final: 0.7767 (mtm-85) REVERT: A 202 THR cc_start: 0.8045 (m) cc_final: 0.7700 (p) REVERT: A 208 ARG cc_start: 0.8248 (mtm180) cc_final: 0.7938 (mtm180) REVERT: A 233 ASP cc_start: 0.7764 (m-30) cc_final: 0.7459 (m-30) REVERT: A 244 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7846 (mt-10) REVERT: B 52 ARG cc_start: 0.7833 (mtt-85) cc_final: 0.7540 (mtt-85) REVERT: B 98 SER cc_start: 0.8117 (m) cc_final: 0.7799 (p) REVERT: B 110 ASN cc_start: 0.8186 (m-40) cc_final: 0.7926 (m-40) REVERT: B 114 CYS cc_start: 0.7868 (p) cc_final: 0.7614 (p) REVERT: B 160 SER cc_start: 0.8255 (t) cc_final: 0.7916 (p) REVERT: B 161 SER cc_start: 0.8548 (t) cc_final: 0.8173 (p) REVERT: B 217 MET cc_start: 0.7756 (pmm) cc_final: 0.7536 (pmm) REVERT: B 221 THR cc_start: 0.8281 (m) cc_final: 0.8056 (t) REVERT: B 226 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 239 ASN cc_start: 0.7902 (m-40) cc_final: 0.7558 (m110) REVERT: B 247 ASP cc_start: 0.7872 (p0) cc_final: 0.7658 (p0) REVERT: B 256 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7869 (mtt90) REVERT: B 277 SER cc_start: 0.8601 (t) cc_final: 0.8175 (p) REVERT: B 312 ASP cc_start: 0.7820 (t0) cc_final: 0.7366 (t0) outliers start: 23 outliers final: 13 residues processed: 252 average time/residue: 0.4537 time to fit residues: 121.6719 Evaluate side-chains 252 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 35 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 29 GLN A 236 GLN B 17 GLN B 88 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** N 35 ASN ** 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 = 0.3767 r_free = 0.3767 target = 0.138414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122067 restraints weight = 11456.493| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.92 r_work: 0.3367 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8734 Z= 0.220 Angle : 0.580 18.445 11837 Z= 0.293 Chirality : 0.041 0.150 1331 Planarity : 0.005 0.057 1458 Dihedral : 5.784 84.479 1279 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.02 % Allowed : 16.09 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1024 helix: 2.33 (0.24), residues: 417 sheet: -0.56 (0.33), residues: 209 loop : -0.72 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 219 TYR 0.021 0.002 TYR N 117 PHE 0.015 0.002 PHE N 68 TRP 0.018 0.002 TRP A 133 HIS 0.006 0.002 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 ( 8730) covalent geometry : angle 0.57984 / 0.29 (11829) SS BOND : bond 0.00162 / 0.08 ( 4) SS BOND : angle 0.99051 / 0.59 ( 8) hydrogen bonds : bond 0.04538 / 3.07 ( 452) hydrogen bonds : angle 5.05619 / 3.69 ( 1302) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 49 ILE cc_start: 0.7967 (mm) cc_final: 0.7753 (mm) REVERT: R 78 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8239 (mtt) REVERT: R 153 LEU cc_start: 0.8004 (mt) cc_final: 0.7793 (mt) REVERT: R 154 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7391 (mp) REVERT: R 159 VAL cc_start: 0.7904 (t) cc_final: 0.7529 (m) REVERT: R 215 THR cc_start: 0.8515 (m) cc_final: 0.8153 (p) REVERT: R 331 TYR cc_start: 0.8395 (m-80) cc_final: 0.8133 (m-80) REVERT: A 24 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7646 (mmmt) REVERT: A 60 MET cc_start: 0.5858 (ttt) cc_final: 0.5576 (ttt) REVERT: A 75 GLN cc_start: 0.7859 (tt0) cc_final: 0.7440 (mt0) REVERT: A 77 ASP cc_start: 0.7833 (m-30) cc_final: 0.7376 (m-30) REVERT: A 93 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8056 (ptt180) REVERT: A 111 ASP cc_start: 0.7842 (t0) cc_final: 0.7477 (t0) REVERT: A 151 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7502 (mt-10) REVERT: A 202 THR cc_start: 0.8066 (m) cc_final: 0.7723 (p) REVERT: A 208 ARG cc_start: 0.8226 (mtm180) cc_final: 0.7932 (mtm180) REVERT: A 222 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7497 (mt-10) REVERT: A 233 ASP cc_start: 0.7771 (m-30) cc_final: 0.7501 (m-30) REVERT: A 244 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7857 (mt-10) REVERT: B 49 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8175 (ptp90) REVERT: B 70 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8192 (pt) REVERT: B 83 ASP cc_start: 0.8373 (t0) cc_final: 0.8157 (t70) REVERT: B 98 SER cc_start: 0.8171 (m) cc_final: 0.7850 (p) REVERT: B 110 ASN cc_start: 0.8295 (m-40) cc_final: 0.8033 (m-40) REVERT: B 114 CYS cc_start: 0.7873 (p) cc_final: 0.7595 (p) REVERT: B 160 SER cc_start: 0.8231 (t) cc_final: 0.7913 (p) REVERT: B 161 SER cc_start: 0.8562 (t) cc_final: 0.8265 (p) REVERT: B 197 ARG cc_start: 0.7912 (mmt180) cc_final: 0.7622 (mtt180) REVERT: B 226 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7896 (mt-10) REVERT: B 230 ASN cc_start: 0.8244 (m-40) cc_final: 0.7734 (m-40) REVERT: B 239 ASN cc_start: 0.7908 (m-40) cc_final: 0.7562 (m110) REVERT: B 256 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7760 (mtt90) REVERT: B 258 ASP cc_start: 0.7765 (t0) cc_final: 0.7472 (t0) REVERT: B 277 SER cc_start: 0.8551 (t) cc_final: 0.8165 (p) REVERT: B 312 ASP cc_start: 0.7834 (t0) cc_final: 0.7359 (t0) REVERT: N 25 SER cc_start: 0.8029 (t) cc_final: 0.7576 (m) outliers start: 27 outliers final: 14 residues processed: 251 average time/residue: 0.5312 time to fit residues: 141.7863 Evaluate side-chains 258 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 29 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 17 GLN B 220 GLN ** N 35 ASN ** 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 = 0.3787 r_free = 0.3787 target = 0.139975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123737 restraints weight = 11423.855| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.93 r_work: 0.3417 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8734 Z= 0.152 Angle : 0.554 19.099 11837 Z= 0.278 Chirality : 0.040 0.146 1331 Planarity : 0.004 0.050 1458 Dihedral : 5.526 81.970 1279 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.46 % Allowed : 17.43 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.26), residues: 1024 helix: 2.50 (0.24), residues: 419 sheet: -0.66 (0.33), residues: 211 loop : -0.64 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 219 TYR 0.020 0.001 TYR N 117 PHE 0.013 0.001 PHE B 199 TRP 0.017 0.002 TRP A 133 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 8730) covalent geometry : angle 0.55390 / 0.28 (11829) SS BOND : bond 0.00073 / 0.04 ( 4) SS BOND : angle 0.74853 / 0.46 ( 8) hydrogen bonds : bond 0.04257 / 2.87 ( 452) hydrogen bonds : angle 4.93553 / 3.60 ( 1302) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8154 (mtt) REVERT: R 154 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7339 (mp) REVERT: R 159 VAL cc_start: 0.7885 (t) cc_final: 0.7552 (m) REVERT: R 270 VAL cc_start: 0.7945 (t) cc_final: 0.7588 (p) REVERT: R 331 TYR cc_start: 0.8455 (m-80) cc_final: 0.8158 (m-80) REVERT: R 338 ARG cc_start: 0.7273 (mtt180) cc_final: 0.6996 (mtt180) REVERT: A 24 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7615 (mmmt) REVERT: A 60 MET cc_start: 0.5869 (ttt) cc_final: 0.5572 (ttt) REVERT: A 75 GLN cc_start: 0.7688 (tt0) cc_final: 0.7260 (mt0) REVERT: A 77 ASP cc_start: 0.7832 (m-30) cc_final: 0.7337 (m-30) REVERT: A 111 ASP cc_start: 0.7818 (t0) cc_final: 0.7471 (t0) REVERT: A 151 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 154 LEU cc_start: 0.8315 (mt) cc_final: 0.8021 (mt) REVERT: A 169 ARG cc_start: 0.8018 (ptp-170) cc_final: 0.7738 (mtm-85) REVERT: A 202 THR cc_start: 0.7994 (m) cc_final: 0.7642 (p) REVERT: A 208 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7950 (mtm180) REVERT: A 222 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7456 (mt-10) REVERT: A 233 ASP cc_start: 0.7737 (m-30) cc_final: 0.7467 (m-30) REVERT: A 244 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7844 (mt-10) REVERT: B 25 CYS cc_start: 0.8120 (m) cc_final: 0.7329 (p) REVERT: B 70 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8148 (pt) REVERT: B 83 ASP cc_start: 0.8309 (t0) cc_final: 0.8069 (t70) REVERT: B 98 SER cc_start: 0.8096 (m) cc_final: 0.7789 (p) REVERT: B 110 ASN cc_start: 0.8261 (m-40) cc_final: 0.8051 (m-40) REVERT: B 114 CYS cc_start: 0.7821 (p) cc_final: 0.7556 (p) REVERT: B 160 SER cc_start: 0.8205 (t) cc_final: 0.7865 (p) REVERT: B 161 SER cc_start: 0.8570 (t) cc_final: 0.8252 (m) REVERT: B 197 ARG cc_start: 0.7814 (mmt180) cc_final: 0.7592 (mtt180) REVERT: B 220 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: B 230 ASN cc_start: 0.8233 (m-40) cc_final: 0.7704 (m-40) REVERT: B 247 ASP cc_start: 0.7748 (p0) cc_final: 0.7495 (p0) REVERT: B 277 SER cc_start: 0.8504 (t) cc_final: 0.8141 (p) REVERT: B 289 TYR cc_start: 0.8443 (m-80) cc_final: 0.8182 (m-80) REVERT: B 307 VAL cc_start: 0.8387 (t) cc_final: 0.8183 (m) REVERT: N 25 SER cc_start: 0.7962 (t) cc_final: 0.7537 (m) outliers start: 22 outliers final: 11 residues processed: 241 average time/residue: 0.5435 time to fit residues: 139.1770 Evaluate side-chains 241 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 226 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 160 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 17 GLN B 75 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.143401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127218 restraints weight = 11577.478| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.96 r_work: 0.3411 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8734 Z= 0.155 Angle : 0.561 19.969 11837 Z= 0.279 Chirality : 0.040 0.147 1331 Planarity : 0.004 0.051 1458 Dihedral : 5.486 81.013 1279 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.57 % Allowed : 18.55 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.26), residues: 1024 helix: 2.50 (0.25), residues: 419 sheet: -0.67 (0.33), residues: 213 loop : -0.60 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 241 TYR 0.019 0.002 TYR N 117 PHE 0.014 0.001 PHE B 199 TRP 0.017 0.002 TRP A 133 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 8730) covalent geometry : angle 0.56076 / 0.28 (11829) SS BOND : bond 0.00065 / 0.03 ( 4) SS BOND : angle 0.72441 / 0.44 ( 8) hydrogen bonds : bond 0.04241 / 2.85 ( 452) hydrogen bonds : angle 4.90556 / 3.59 ( 1302) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8195 (mtt) REVERT: R 154 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7332 (mp) REVERT: R 159 VAL cc_start: 0.7886 (t) cc_final: 0.7555 (m) REVERT: R 270 VAL cc_start: 0.7953 (t) cc_final: 0.7601 (p) REVERT: R 331 TYR cc_start: 0.8439 (m-80) cc_final: 0.8164 (m-80) REVERT: R 338 ARG cc_start: 0.7279 (mtt180) cc_final: 0.7007 (mtt180) REVERT: A 24 LYS cc_start: 0.7860 (mmmt) cc_final: 0.7642 (mmmt) REVERT: A 60 MET cc_start: 0.5887 (ttt) cc_final: 0.5592 (ttt) REVERT: A 75 GLN cc_start: 0.7689 (tt0) cc_final: 0.7249 (mt0) REVERT: A 77 ASP cc_start: 0.7865 (m-30) cc_final: 0.7333 (m-30) REVERT: A 111 ASP cc_start: 0.7837 (t0) cc_final: 0.7490 (t0) REVERT: A 151 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7513 (mt-10) REVERT: A 169 ARG cc_start: 0.8009 (ptp-170) cc_final: 0.7746 (mtp-110) REVERT: A 202 THR cc_start: 0.7895 (m) cc_final: 0.7542 (p) REVERT: A 208 ARG cc_start: 0.8210 (mtm180) cc_final: 0.7971 (mtm180) REVERT: A 222 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7465 (mt-10) REVERT: A 233 ASP cc_start: 0.7743 (m-30) cc_final: 0.7466 (m-30) REVERT: A 244 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7867 (mt-10) REVERT: B 25 CYS cc_start: 0.8133 (m) cc_final: 0.7347 (p) REVERT: B 70 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8147 (pt) REVERT: B 83 ASP cc_start: 0.8317 (t0) cc_final: 0.8099 (t70) REVERT: B 98 SER cc_start: 0.8114 (m) cc_final: 0.7813 (p) REVERT: B 110 ASN cc_start: 0.8296 (m-40) cc_final: 0.8024 (m110) REVERT: B 114 CYS cc_start: 0.7803 (p) cc_final: 0.7552 (p) REVERT: B 161 SER cc_start: 0.8604 (t) cc_final: 0.8165 (m) REVERT: B 197 ARG cc_start: 0.7854 (mmt180) cc_final: 0.7605 (mtt180) REVERT: B 239 ASN cc_start: 0.7963 (m110) cc_final: 0.7644 (m110) REVERT: B 256 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7745 (mtt180) REVERT: B 259 GLN cc_start: 0.8366 (pt0) cc_final: 0.7477 (pt0) REVERT: B 277 SER cc_start: 0.8509 (t) cc_final: 0.8144 (p) REVERT: B 289 TYR cc_start: 0.8408 (m-80) cc_final: 0.8157 (m-80) REVERT: B 307 VAL cc_start: 0.8427 (t) cc_final: 0.8201 (m) REVERT: N 25 SER cc_start: 0.7981 (t) cc_final: 0.7554 (m) outliers start: 23 outliers final: 15 residues processed: 235 average time/residue: 0.5481 time to fit residues: 136.5732 Evaluate side-chains 240 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 7 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 29 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 75 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.143870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.127835 restraints weight = 11423.611| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.94 r_work: 0.3430 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8734 Z= 0.142 Angle : 0.543 18.061 11837 Z= 0.273 Chirality : 0.039 0.142 1331 Planarity : 0.004 0.052 1458 Dihedral : 5.366 79.093 1279 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.13 % Allowed : 17.99 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.27), residues: 1024 helix: 2.56 (0.24), residues: 419 sheet: -0.63 (0.33), residues: 216 loop : -0.59 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 241 TYR 0.018 0.001 TYR N 117 PHE 0.013 0.001 PHE B 199 TRP 0.017 0.002 TRP A 133 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 8730) covalent geometry : angle 0.54299 / 0.27 (11829) SS BOND : bond 0.00058 / 0.03 ( 4) SS BOND : angle 0.69464 / 0.42 ( 8) hydrogen bonds : bond 0.04125 / 2.77 ( 452) hydrogen bonds : angle 4.85745 / 3.55 ( 1302) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8208 (mtt) REVERT: R 154 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7315 (mp) REVERT: R 270 VAL cc_start: 0.7966 (t) cc_final: 0.7615 (p) REVERT: R 331 TYR cc_start: 0.8415 (m-80) cc_final: 0.8191 (m-80) REVERT: R 338 ARG cc_start: 0.7297 (mtt180) cc_final: 0.7019 (mtt180) REVERT: A 24 LYS cc_start: 0.7827 (mmmt) cc_final: 0.7538 (tppp) REVERT: A 60 MET cc_start: 0.5884 (ttt) cc_final: 0.5591 (ttt) REVERT: A 75 GLN cc_start: 0.7652 (tt0) cc_final: 0.7193 (mt0) REVERT: A 77 ASP cc_start: 0.7845 (m-30) cc_final: 0.7315 (m-30) REVERT: A 111 ASP cc_start: 0.7839 (t0) cc_final: 0.7473 (t0) REVERT: A 151 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7522 (mt-10) REVERT: A 169 ARG cc_start: 0.8000 (ptp-170) cc_final: 0.7742 (mtp-110) REVERT: A 202 THR cc_start: 0.7898 (m) cc_final: 0.7544 (p) REVERT: A 208 ARG cc_start: 0.8208 (mtm180) cc_final: 0.7974 (mtm180) REVERT: A 233 ASP cc_start: 0.7740 (m-30) cc_final: 0.7473 (m-30) REVERT: A 244 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7857 (mt-10) REVERT: B 20 ASP cc_start: 0.7280 (m-30) cc_final: 0.6865 (m-30) REVERT: B 25 CYS cc_start: 0.8149 (m) cc_final: 0.7370 (p) REVERT: B 70 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8132 (pt) REVERT: B 83 ASP cc_start: 0.8312 (t0) cc_final: 0.8086 (t70) REVERT: B 98 SER cc_start: 0.8158 (m) cc_final: 0.7849 (p) REVERT: B 110 ASN cc_start: 0.8316 (m-40) cc_final: 0.8081 (m110) REVERT: B 161 SER cc_start: 0.8473 (t) cc_final: 0.8162 (m) REVERT: B 197 ARG cc_start: 0.7894 (mmt180) cc_final: 0.7634 (mtt180) REVERT: B 239 ASN cc_start: 0.7970 (m110) cc_final: 0.7676 (m110) REVERT: B 256 ARG cc_start: 0.7955 (mtt180) cc_final: 0.7726 (mtt180) REVERT: B 259 GLN cc_start: 0.8301 (pt0) cc_final: 0.7442 (pt0) REVERT: B 277 SER cc_start: 0.8505 (t) cc_final: 0.8135 (p) REVERT: B 289 TYR cc_start: 0.8377 (m-80) cc_final: 0.8119 (m-80) REVERT: B 307 VAL cc_start: 0.8421 (t) cc_final: 0.8199 (m) REVERT: N 25 SER cc_start: 0.7974 (t) cc_final: 0.7621 (m) outliers start: 28 outliers final: 15 residues processed: 231 average time/residue: 0.5422 time to fit residues: 132.7705 Evaluate side-chains 242 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** 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 = 0.3784 r_free = 0.3784 target = 0.139661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123320 restraints weight = 11390.008| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.92 r_work: 0.3392 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8734 Z= 0.171 Angle : 0.567 19.376 11837 Z= 0.283 Chirality : 0.040 0.150 1331 Planarity : 0.004 0.053 1458 Dihedral : 5.414 78.076 1279 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.57 % Allowed : 18.77 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.27), residues: 1024 helix: 2.62 (0.24), residues: 413 sheet: -0.67 (0.33), residues: 220 loop : -0.58 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.026 0.002 TYR N 60 PHE 0.013 0.001 PHE R 288 TRP 0.016 0.002 TRP A 133 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 8730) covalent geometry : angle 0.56666 / 0.28 (11829) SS BOND : bond 0.00086 / 0.04 ( 4) SS BOND : angle 0.80589 / 0.48 ( 8) hydrogen bonds : bond 0.04259 / 2.86 ( 452) hydrogen bonds : angle 4.89561 / 3.58 ( 1302) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8251 (mtt) REVERT: R 270 VAL cc_start: 0.7964 (t) cc_final: 0.7611 (p) REVERT: R 331 TYR cc_start: 0.8435 (m-80) cc_final: 0.8214 (m-80) REVERT: R 338 ARG cc_start: 0.7293 (mtt180) cc_final: 0.7022 (mtt180) REVERT: A 24 LYS cc_start: 0.7845 (mmmt) cc_final: 0.7629 (mmmt) REVERT: A 60 MET cc_start: 0.5900 (ttt) cc_final: 0.5592 (ttt) REVERT: A 75 GLN cc_start: 0.7733 (tt0) cc_final: 0.7272 (mt0) REVERT: A 77 ASP cc_start: 0.7850 (m-30) cc_final: 0.7321 (m-30) REVERT: A 111 ASP cc_start: 0.7823 (t0) cc_final: 0.7473 (t0) REVERT: A 169 ARG cc_start: 0.7971 (ptp-170) cc_final: 0.7714 (mtp-110) REVERT: A 202 THR cc_start: 0.7923 (m) cc_final: 0.7540 (p) REVERT: A 208 ARG cc_start: 0.8205 (mtm180) cc_final: 0.7966 (mtm180) REVERT: A 233 ASP cc_start: 0.7758 (m-30) cc_final: 0.7488 (m-30) REVERT: A 244 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7881 (mt-10) REVERT: B 20 ASP cc_start: 0.7274 (m-30) cc_final: 0.6849 (m-30) REVERT: B 70 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8159 (pt) REVERT: B 83 ASP cc_start: 0.8320 (t0) cc_final: 0.8079 (t70) REVERT: B 98 SER cc_start: 0.8142 (m) cc_final: 0.7813 (p) REVERT: B 189 SER cc_start: 0.8086 (m) cc_final: 0.7687 (p) REVERT: B 197 ARG cc_start: 0.7917 (mmt180) cc_final: 0.7697 (mtt180) REVERT: B 200 VAL cc_start: 0.8830 (p) cc_final: 0.8515 (m) REVERT: B 239 ASN cc_start: 0.7965 (m110) cc_final: 0.7654 (m110) REVERT: B 256 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7760 (mtt180) REVERT: B 277 SER cc_start: 0.8517 (t) cc_final: 0.8164 (p) REVERT: B 289 TYR cc_start: 0.8398 (m-80) cc_final: 0.8094 (m-80) REVERT: B 307 VAL cc_start: 0.8420 (t) cc_final: 0.8206 (m) REVERT: N 25 SER cc_start: 0.8022 (t) cc_final: 0.7586 (m) REVERT: N 83 MET cc_start: 0.7697 (mtp) cc_final: 0.7487 (mtp) outliers start: 23 outliers final: 13 residues processed: 233 average time/residue: 0.5452 time to fit residues: 134.5256 Evaluate side-chains 239 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 6 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 75 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** 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 = 0.3793 r_free = 0.3793 target = 0.140960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124888 restraints weight = 11421.963| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.95 r_work: 0.3423 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8734 Z= 0.151 Angle : 0.562 20.539 11837 Z= 0.278 Chirality : 0.040 0.150 1331 Planarity : 0.004 0.052 1458 Dihedral : 5.366 76.258 1279 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.79 % Allowed : 20.00 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.27), residues: 1024 helix: 2.61 (0.24), residues: 413 sheet: -0.70 (0.34), residues: 218 loop : -0.55 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.019 0.002 TYR N 117 PHE 0.013 0.001 PHE R 288 TRP 0.016 0.002 TRP A 133 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 8730) covalent geometry : angle 0.56214 / 0.28 (11829) SS BOND : bond 0.00079 / 0.04 ( 4) SS BOND : angle 0.72441 / 0.44 ( 8) hydrogen bonds : bond 0.04167 / 2.80 ( 452) hydrogen bonds : angle 4.86134 / 3.56 ( 1302) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 225 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8249 (mtt) REVERT: R 270 VAL cc_start: 0.7978 (t) cc_final: 0.7626 (p) REVERT: R 331 TYR cc_start: 0.8425 (m-80) cc_final: 0.8205 (m-80) REVERT: R 338 ARG cc_start: 0.7301 (mtt180) cc_final: 0.7029 (mtt180) REVERT: A 24 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7617 (mmmt) REVERT: A 57 VAL cc_start: 0.8137 (t) cc_final: 0.7756 (m) REVERT: A 60 MET cc_start: 0.5813 (ttt) cc_final: 0.5501 (ttt) REVERT: A 75 GLN cc_start: 0.7715 (tt0) cc_final: 0.7259 (mt0) REVERT: A 77 ASP cc_start: 0.7843 (m-30) cc_final: 0.7335 (m-30) REVERT: A 93 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7897 (ptt180) REVERT: A 111 ASP cc_start: 0.7814 (t0) cc_final: 0.7503 (t0) REVERT: A 146 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7614 (mt0) REVERT: A 169 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7708 (mtp-110) REVERT: A 208 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7991 (mtm180) REVERT: A 233 ASP cc_start: 0.7738 (m-30) cc_final: 0.7478 (m-30) REVERT: A 244 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7886 (mt-10) REVERT: B 20 ASP cc_start: 0.7235 (m-30) cc_final: 0.6824 (m-30) REVERT: B 70 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8203 (pt) REVERT: B 83 ASP cc_start: 0.8323 (t0) cc_final: 0.8084 (t70) REVERT: B 96 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.8073 (mtm-85) REVERT: B 98 SER cc_start: 0.8146 (m) cc_final: 0.7795 (p) REVERT: B 161 SER cc_start: 0.8238 (t) cc_final: 0.8012 (p) REVERT: B 189 SER cc_start: 0.8075 (m) cc_final: 0.7648 (p) REVERT: B 200 VAL cc_start: 0.8867 (p) cc_final: 0.8558 (m) REVERT: B 239 ASN cc_start: 0.7984 (m110) cc_final: 0.7732 (m110) REVERT: B 274 THR cc_start: 0.8151 (m) cc_final: 0.7911 (p) REVERT: B 277 SER cc_start: 0.8516 (t) cc_final: 0.8154 (p) REVERT: B 289 TYR cc_start: 0.8379 (m-80) cc_final: 0.8082 (m-80) REVERT: B 307 VAL cc_start: 0.8442 (t) cc_final: 0.8215 (m) REVERT: N 25 SER cc_start: 0.8031 (t) cc_final: 0.7598 (m) REVERT: N 83 MET cc_start: 0.7679 (mtp) cc_final: 0.7466 (mtp) outliers start: 16 outliers final: 12 residues processed: 229 average time/residue: 0.5089 time to fit residues: 123.5696 Evaluate side-chains 238 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 78 MET Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 49 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** 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 = 0.3775 r_free = 0.3775 target = 0.138925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122628 restraints weight = 11354.287| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.91 r_work: 0.3385 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8734 Z= 0.191 Angle : 0.600 21.446 11837 Z= 0.295 Chirality : 0.041 0.159 1331 Planarity : 0.004 0.056 1458 Dihedral : 5.475 75.384 1279 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.79 % Allowed : 20.34 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.27), residues: 1024 helix: 2.48 (0.24), residues: 413 sheet: -0.71 (0.33), residues: 227 loop : -0.56 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.025 0.002 TYR N 60 PHE 0.014 0.002 PHE R 288 TRP 0.015 0.002 TRP R 80 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 8730) covalent geometry : angle 0.60000 / 0.30 (11829) SS BOND : bond 0.00095 / 0.05 ( 4) SS BOND : angle 0.89866 / 0.54 ( 8) hydrogen bonds : bond 0.04337 / 2.92 ( 452) hydrogen bonds : angle 4.96421 / 3.63 ( 1302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3109.63 seconds wall clock time: 53 minutes 38.67 seconds (3218.67 seconds total)