Starting phenix.real_space_refine on Thu Mar 13 11:36:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ljc_23390/03_2025/7ljc_23390.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ljc_23390/03_2025/7ljc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ljc_23390/03_2025/7ljc_23390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ljc_23390/03_2025/7ljc_23390.map" model { file = "/net/cci-nas-00/data/ceres_data/7ljc_23390/03_2025/7ljc_23390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ljc_23390/03_2025/7ljc_23390.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.58, per 1000 atoms: 0.65 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: 2.67 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.94 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: 2.36 Time building geometry restraints manager: 3.04 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: 5350 17.55 - 35.09: 135 35.09 - 52.64: 34 52.64 - 70.18: 4 70.18 - 87.73: 2 Dihedral angle restraints: 5525 sinusoidal: 2489 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 5522 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: 0.460 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.790 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 8730 Z= 0.346 Angle : 1.005 9.518 11829 Z= 0.544 Chirality : 0.068 0.457 1331 Planarity : 0.009 0.156 1458 Dihedral : 9.081 87.728 3541 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (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 TRP 0.032 0.003 TRP A 133 HIS 0.009 0.003 HIS A 209 PHE 0.030 0.003 PHE B 278 TYR 0.022 0.002 TYR N 95 ARG 0.012 0.001 ARG A 194 *********************** 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 : 0.918 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: 0.8319 (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: 0.7550 (tt0) REVERT: A 142 PHE cc_start: 0.8762 (m-80) cc_final: 0.8436 (m-80) REVERT: A 169 ARG cc_start: 0.8271 (ptp-170) cc_final: 0.7917 (ptp-170) REVERT: A 202 THR cc_start: 0.8451 (m) cc_final: 0.8031 (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: 0.8363 (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: 0.8115 (p) REVERT: B 52 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8176 (mtt-85) REVERT: B 98 SER cc_start: 0.8371 (m) cc_final: 0.7990 (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: 0.7746 (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: 0.7770 (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: 0.7372 (t0) REVERT: B 262 MET cc_start: 0.8576 (ttm) cc_final: 0.8308 (ttm) REVERT: B 264 TYR cc_start: 0.8593 (m-80) cc_final: 0.8101 (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: 0.8243 (m-80) REVERT: B 312 ASP cc_start: 0.8630 (t0) cc_final: 0.8362 (t0) REVERT: N 112 SER cc_start: 0.8084 (p) cc_final: 0.7721 (m) outliers start: 1 outliers final: 3 residues processed: 294 average time/residue: 1.0999 time to fit residues: 347.1899 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 : 0.938 ------------------------------------------------------------------------------- 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 85 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3852 r_free = 0.3852 target = 0.144977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.128835 restraints weight = 11515.212| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.02 r_work: 0.3524 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8730 Z= 0.197 Angle : 0.565 15.999 11829 Z= 0.292 Chirality : 0.041 0.208 1331 Planarity : 0.005 0.048 1458 Dihedral : 7.556 87.227 1650 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.02 % Allowed : 10.50 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1024 helix: 2.31 (0.23), residues: 411 sheet: -0.38 (0.34), residues: 214 loop : -1.24 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.009 0.001 HIS A 82 PHE 0.020 0.002 PHE B 199 TYR 0.013 0.001 TYR B 124 ARG 0.008 0.001 ARG B 49 *********************** 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 285 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 153 LEU cc_start: 0.8079 (mt) cc_final: 0.7839 (mt) REVERT: R 159 VAL cc_start: 0.8062 (t) cc_final: 0.7681 (m) REVERT: R 270 VAL cc_start: 0.7839 (t) cc_final: 0.7541 (p) REVERT: R 331 TYR cc_start: 0.7979 (m-80) cc_final: 0.7699 (m-80) REVERT: A 24 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7706 (mmmt) REVERT: A 70 PHE cc_start: 0.7792 (m-80) cc_final: 0.7563 (m-10) REVERT: A 77 ASP cc_start: 0.7629 (m-30) cc_final: 0.7313 (m-30) REVERT: A 93 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8188 (ptp90) REVERT: A 111 ASP cc_start: 0.7778 (t0) cc_final: 0.7001 (t0) REVERT: A 114 ASP cc_start: 0.7511 (m-30) cc_final: 0.6709 (m-30) REVERT: A 142 PHE cc_start: 0.8479 (m-80) cc_final: 0.8246 (m-80) REVERT: A 161 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7864 (mt-10) REVERT: A 169 ARG cc_start: 0.7953 (ptp-170) cc_final: 0.7565 (ptp-170) REVERT: A 200 ILE cc_start: 0.8424 (mt) cc_final: 0.8209 (mm) REVERT: A 202 THR cc_start: 0.8002 (m) cc_final: 0.7576 (p) REVERT: A 208 ARG cc_start: 0.8181 (mtm180) cc_final: 0.7847 (mtm180) REVERT: A 229 ASN cc_start: 0.8265 (m-40) cc_final: 0.7729 (m-40) REVERT: A 233 ASP cc_start: 0.7710 (m-30) cc_final: 0.7356 (m-30) REVERT: A 244 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7564 (mt-10) REVERT: B 52 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7442 (mtt-85) REVERT: B 70 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8044 (pt) REVERT: B 98 SER cc_start: 0.8084 (m) cc_final: 0.7561 (p) REVERT: B 114 CYS cc_start: 0.7695 (p) cc_final: 0.7351 (p) REVERT: B 124 TYR cc_start: 0.8386 (m-80) cc_final: 0.8062 (m-80) REVERT: B 137 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.6882 (mmm-85) REVERT: B 158 VAL cc_start: 0.7765 (t) cc_final: 0.7546 (p) REVERT: B 186 ASP cc_start: 0.7830 (m-30) cc_final: 0.7548 (m-30) REVERT: B 195 ASP cc_start: 0.7706 (p0) cc_final: 0.7467 (p0) REVERT: B 221 THR cc_start: 0.8170 (m) cc_final: 0.7870 (t) REVERT: B 226 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7884 (mt-10) REVERT: B 239 ASN cc_start: 0.7687 (m-40) cc_final: 0.7308 (m-40) REVERT: B 247 ASP cc_start: 0.7767 (p0) cc_final: 0.7552 (p0) REVERT: B 254 ASP cc_start: 0.7613 (t0) cc_final: 0.7162 (t70) REVERT: B 256 ARG cc_start: 0.7907 (mtt90) cc_final: 0.7657 (mtt90) REVERT: B 258 ASP cc_start: 0.7313 (t0) cc_final: 0.6832 (t0) REVERT: B 277 SER cc_start: 0.8646 (t) cc_final: 0.8412 (t) REVERT: B 289 TYR cc_start: 0.8454 (m-80) cc_final: 0.8195 (m-80) REVERT: B 312 ASP cc_start: 0.7720 (t0) cc_final: 0.7407 (t0) REVERT: N 112 SER cc_start: 0.7991 (p) cc_final: 0.7640 (m) outliers start: 27 outliers final: 10 residues processed: 269 average time/residue: 1.1304 time to fit residues: 324.2875 Evaluate side-chains 255 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 243 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 93 ARG 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 23 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 110 ASN B 220 GLN B 259 GLN N 5 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 = 0.3794 r_free = 0.3794 target = 0.140232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123602 restraints weight = 11487.751| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.98 r_work: 0.3439 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8730 Z= 0.279 Angle : 0.587 17.932 11829 Z= 0.297 Chirality : 0.042 0.162 1331 Planarity : 0.004 0.046 1458 Dihedral : 7.162 87.130 1648 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.68 % Allowed : 13.63 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1024 helix: 2.42 (0.24), residues: 418 sheet: -0.47 (0.34), residues: 198 loop : -1.07 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 133 HIS 0.008 0.001 HIS A 209 PHE 0.020 0.002 PHE B 199 TYR 0.012 0.002 TYR B 59 ARG 0.010 0.001 ARG A 241 *********************** 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 283 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 259 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 153 LEU cc_start: 0.8007 (mt) cc_final: 0.7779 (mt) REVERT: R 215 THR cc_start: 0.8479 (m) cc_final: 0.8188 (p) REVERT: R 270 VAL cc_start: 0.7960 (t) cc_final: 0.7652 (p) REVERT: R 331 TYR cc_start: 0.8286 (m-80) cc_final: 0.8011 (m-80) REVERT: A 24 LYS cc_start: 0.7934 (mmmt) cc_final: 0.7685 (mmmt) REVERT: A 60 MET cc_start: 0.6001 (ttt) cc_final: 0.5704 (ttt) REVERT: A 77 ASP cc_start: 0.7679 (m-30) cc_final: 0.7364 (m-30) REVERT: A 93 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8163 (ptt180) REVERT: A 111 ASP cc_start: 0.7829 (t0) cc_final: 0.7579 (t0) REVERT: A 117 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7994 (mtm110) REVERT: A 137 ILE cc_start: 0.8163 (pp) cc_final: 0.7680 (mt) REVERT: A 151 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7567 (mt-10) REVERT: A 169 ARG cc_start: 0.7973 (ptp-170) cc_final: 0.7627 (mtm-85) REVERT: A 202 THR cc_start: 0.8036 (m) cc_final: 0.7653 (p) REVERT: A 208 ARG cc_start: 0.8262 (mtm180) cc_final: 0.7945 (mtm180) REVERT: A 233 ASP cc_start: 0.7762 (m-30) cc_final: 0.7447 (m-30) REVERT: A 244 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7839 (mt-10) REVERT: B 25 CYS cc_start: 0.8120 (m) cc_final: 0.7459 (p) REVERT: B 52 ARG cc_start: 0.7798 (mtt-85) cc_final: 0.7485 (mtt-85) REVERT: B 83 ASP cc_start: 0.8314 (t0) cc_final: 0.8045 (t70) REVERT: B 98 SER cc_start: 0.8179 (m) cc_final: 0.7751 (p) REVERT: B 114 CYS cc_start: 0.7827 (p) cc_final: 0.7563 (p) REVERT: B 195 ASP cc_start: 0.7747 (p0) cc_final: 0.7494 (p0) REVERT: B 197 ARG cc_start: 0.7826 (mmt180) cc_final: 0.7370 (mtt180) REVERT: B 221 THR cc_start: 0.8268 (m) cc_final: 0.8042 (t) REVERT: B 226 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7817 (mt-10) REVERT: B 245 SER cc_start: 0.8372 (m) cc_final: 0.8023 (t) REVERT: B 258 ASP cc_start: 0.7588 (t0) cc_final: 0.7192 (t0) REVERT: B 259 GLN cc_start: 0.8479 (pt0) cc_final: 0.7996 (pt0) REVERT: B 277 SER cc_start: 0.8621 (t) cc_final: 0.8263 (p) REVERT: B 289 TYR cc_start: 0.8491 (m-80) cc_final: 0.8289 (m-80) REVERT: B 312 ASP cc_start: 0.7746 (t0) cc_final: 0.7335 (t0) REVERT: N 112 SER cc_start: 0.8277 (p) cc_final: 0.7995 (m) outliers start: 24 outliers final: 15 residues processed: 265 average time/residue: 1.1516 time to fit residues: 324.9162 Evaluate side-chains 249 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 133 ARG 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 75 GLN Chi-restraints excluded: chain A residue 93 ARG 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 N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 131 ASN A 236 GLN B 88 ASN B 110 ASN B 220 GLN B 295 ASN B 340 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.142792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126748 restraints weight = 11531.925| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.99 r_work: 0.3430 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8730 Z= 0.234 Angle : 0.556 20.258 11829 Z= 0.277 Chirality : 0.040 0.148 1331 Planarity : 0.004 0.049 1458 Dihedral : 6.683 85.829 1648 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.35 % Allowed : 15.53 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1024 helix: 2.52 (0.24), residues: 418 sheet: -0.53 (0.33), residues: 198 loop : -0.84 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 133 HIS 0.005 0.001 HIS A 209 PHE 0.015 0.001 PHE B 199 TYR 0.010 0.001 TYR A 163 ARG 0.009 0.000 ARG A 241 *********************** 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 251 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8177 (mtt) REVERT: R 153 LEU cc_start: 0.8008 (mt) cc_final: 0.7775 (mt) REVERT: R 159 VAL cc_start: 0.7918 (t) cc_final: 0.7548 (m) REVERT: R 270 VAL cc_start: 0.7953 (t) cc_final: 0.7608 (p) REVERT: R 331 TYR cc_start: 0.8328 (m-80) cc_final: 0.8057 (m-80) REVERT: A 24 LYS cc_start: 0.7857 (mmmt) cc_final: 0.7548 (tppp) REVERT: A 60 MET cc_start: 0.5902 (ttt) cc_final: 0.5605 (ttt) REVERT: A 77 ASP cc_start: 0.7661 (m-30) cc_final: 0.7286 (m-30) REVERT: A 89 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7452 (mm-40) REVERT: A 93 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8031 (ptt180) REVERT: A 111 ASP cc_start: 0.7843 (t0) cc_final: 0.7525 (t0) REVERT: A 117 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7976 (mtp180) REVERT: A 146 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7713 (mm-40) REVERT: A 151 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7542 (mt-10) REVERT: A 199 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8043 (ttp-170) REVERT: A 200 ILE cc_start: 0.8576 (mt) cc_final: 0.8339 (mm) REVERT: A 202 THR cc_start: 0.8024 (m) cc_final: 0.7624 (p) REVERT: A 208 ARG cc_start: 0.8225 (mtm180) cc_final: 0.7912 (mtm180) REVERT: A 233 ASP cc_start: 0.7763 (m-30) cc_final: 0.7467 (m-30) REVERT: A 244 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7803 (mt-10) REVERT: B 52 ARG cc_start: 0.7769 (mtt-85) cc_final: 0.7470 (mtt-85) REVERT: B 98 SER cc_start: 0.8097 (m) cc_final: 0.7671 (p) REVERT: B 114 CYS cc_start: 0.7853 (p) cc_final: 0.7591 (p) REVERT: B 158 VAL cc_start: 0.7918 (t) cc_final: 0.7709 (p) REVERT: B 160 SER cc_start: 0.8219 (t) cc_final: 0.7853 (p) REVERT: B 161 SER cc_start: 0.8341 (t) cc_final: 0.8014 (p) REVERT: B 197 ARG cc_start: 0.7808 (mmt180) cc_final: 0.7591 (mtt180) REVERT: B 219 ARG cc_start: 0.8232 (mtp85) cc_final: 0.8010 (ttm-80) REVERT: B 221 THR cc_start: 0.8248 (m) cc_final: 0.8020 (t) REVERT: B 245 SER cc_start: 0.8362 (m) cc_final: 0.8139 (p) REVERT: B 277 SER cc_start: 0.8575 (t) cc_final: 0.8209 (p) REVERT: B 289 TYR cc_start: 0.8483 (m-80) cc_final: 0.8232 (m-80) REVERT: B 312 ASP cc_start: 0.7776 (t0) cc_final: 0.7364 (t0) outliers start: 21 outliers final: 12 residues processed: 236 average time/residue: 1.1815 time to fit residues: 296.7530 Evaluate side-chains 232 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 196 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 110 VAL Chi-restraints excluded: chain A residue 221 THR 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 49 SER 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 22 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.0570 chunk 23 optimal weight: 0.7980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN B 17 GLN B 88 ASN B 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125114 restraints weight = 11494.199| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.95 r_work: 0.3436 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8730 Z= 0.205 Angle : 0.532 18.313 11829 Z= 0.267 Chirality : 0.039 0.144 1331 Planarity : 0.004 0.046 1458 Dihedral : 6.277 84.284 1646 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.13 % Allowed : 14.64 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1024 helix: 2.59 (0.24), residues: 419 sheet: -0.63 (0.33), residues: 211 loop : -0.70 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS A 82 PHE 0.015 0.001 PHE B 199 TYR 0.016 0.001 TYR N 117 ARG 0.006 0.000 ARG A 241 *********************** 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 264 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8247 (mtt) REVERT: R 133 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8374 (mtm-85) REVERT: R 154 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7343 (mp) REVERT: R 270 VAL cc_start: 0.7954 (t) cc_final: 0.7596 (p) REVERT: R 331 TYR cc_start: 0.8353 (m-80) cc_final: 0.8105 (m-80) REVERT: A 24 LYS cc_start: 0.7844 (mmmt) cc_final: 0.7534 (tppp) REVERT: A 36 VAL cc_start: 0.8373 (p) cc_final: 0.8136 (t) REVERT: A 60 MET cc_start: 0.5902 (ttt) cc_final: 0.5591 (ttt) REVERT: A 77 ASP cc_start: 0.7656 (m-30) cc_final: 0.7280 (m-30) REVERT: A 93 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8059 (ptt180) REVERT: A 111 ASP cc_start: 0.7848 (t0) cc_final: 0.7488 (t0) REVERT: A 117 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7938 (mtm110) REVERT: A 146 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7556 (mm110) REVERT: A 151 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7528 (mt-10) REVERT: A 199 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8040 (ttp-170) REVERT: A 200 ILE cc_start: 0.8559 (mt) cc_final: 0.8353 (mm) REVERT: A 202 THR cc_start: 0.7906 (m) cc_final: 0.7525 (p) REVERT: A 208 ARG cc_start: 0.8206 (mtm180) cc_final: 0.7919 (mtm180) REVERT: A 225 ARG cc_start: 0.7862 (tpp-160) cc_final: 0.7515 (mmt-90) REVERT: A 233 ASP cc_start: 0.7744 (m-30) cc_final: 0.7441 (m-30) REVERT: A 244 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 49 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8210 (ptp90) REVERT: B 98 SER cc_start: 0.8065 (m) cc_final: 0.7758 (p) REVERT: B 114 CYS cc_start: 0.7823 (p) cc_final: 0.7553 (p) REVERT: B 160 SER cc_start: 0.8236 (t) cc_final: 0.7884 (p) REVERT: B 161 SER cc_start: 0.8474 (t) cc_final: 0.8081 (p) REVERT: B 197 ARG cc_start: 0.7902 (mmt180) cc_final: 0.7586 (mtt180) REVERT: B 219 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7972 (ttm-80) REVERT: B 221 THR cc_start: 0.8216 (m) cc_final: 0.8000 (t) REVERT: B 239 ASN cc_start: 0.7891 (m110) cc_final: 0.7556 (m110) REVERT: B 277 SER cc_start: 0.8569 (t) cc_final: 0.8209 (p) REVERT: B 285 LEU cc_start: 0.8369 (tp) cc_final: 0.8155 (tt) REVERT: B 289 TYR cc_start: 0.8483 (m-80) cc_final: 0.8217 (m-80) REVERT: N 25 SER cc_start: 0.7910 (OUTLIER) cc_final: 0.7493 (m) outliers start: 28 outliers final: 18 residues processed: 243 average time/residue: 1.2025 time to fit residues: 311.0119 Evaluate side-chains 247 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 75 GLN Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 71 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 20 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 236 GLN B 17 GLN B 75 GLN B 88 ASN B 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124616 restraints weight = 11373.287| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.93 r_work: 0.3433 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8730 Z= 0.224 Angle : 0.548 19.407 11829 Z= 0.272 Chirality : 0.040 0.145 1331 Planarity : 0.004 0.048 1458 Dihedral : 6.161 83.615 1646 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.35 % Allowed : 16.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1024 helix: 2.58 (0.24), residues: 419 sheet: -0.67 (0.33), residues: 211 loop : -0.63 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 133 HIS 0.005 0.001 HIS A 82 PHE 0.014 0.001 PHE A 74 TYR 0.018 0.001 TYR N 117 ARG 0.007 0.000 ARG A 241 *********************** 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 262 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8255 (mtt) REVERT: R 133 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8359 (mtm-85) REVERT: R 154 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7353 (mp) REVERT: R 270 VAL cc_start: 0.7984 (t) cc_final: 0.7620 (p) REVERT: R 331 TYR cc_start: 0.8361 (m-80) cc_final: 0.8099 (m-80) REVERT: A 24 LYS cc_start: 0.7849 (mmmt) cc_final: 0.7553 (tppp) REVERT: A 36 VAL cc_start: 0.8369 (p) cc_final: 0.8154 (t) REVERT: A 60 MET cc_start: 0.5884 (ttt) cc_final: 0.5572 (ttt) REVERT: A 77 ASP cc_start: 0.7648 (m-30) cc_final: 0.7278 (m-30) REVERT: A 93 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8057 (ptt180) REVERT: A 111 ASP cc_start: 0.7852 (t0) cc_final: 0.7474 (t0) REVERT: A 117 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7979 (mtm110) REVERT: A 132 ARG cc_start: 0.7697 (ttt180) cc_final: 0.7477 (ttt180) REVERT: A 151 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7529 (mt-10) REVERT: A 199 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8030 (ttp-170) REVERT: A 200 ILE cc_start: 0.8556 (mt) cc_final: 0.8324 (mm) REVERT: A 202 THR cc_start: 0.7950 (m) cc_final: 0.7575 (p) REVERT: A 208 ARG cc_start: 0.8206 (mtm180) cc_final: 0.7934 (mtm180) REVERT: A 225 ARG cc_start: 0.7886 (tpp-160) cc_final: 0.7525 (mmt-90) REVERT: A 233 ASP cc_start: 0.7725 (m-30) cc_final: 0.7443 (m-30) REVERT: A 244 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7662 (mt-10) REVERT: B 49 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8137 (ptp90) REVERT: B 83 ASP cc_start: 0.8293 (t0) cc_final: 0.7981 (t70) REVERT: B 98 SER cc_start: 0.8085 (m) cc_final: 0.7781 (p) REVERT: B 114 CYS cc_start: 0.7840 (p) cc_final: 0.7565 (p) REVERT: B 160 SER cc_start: 0.8240 (t) cc_final: 0.7892 (p) REVERT: B 161 SER cc_start: 0.8497 (t) cc_final: 0.8007 (t) REVERT: B 195 ASP cc_start: 0.7693 (p0) cc_final: 0.7445 (p0) REVERT: B 197 ARG cc_start: 0.7902 (mmt180) cc_final: 0.7372 (mtt180) REVERT: B 219 ARG cc_start: 0.8206 (mtp85) cc_final: 0.8004 (ttm-80) REVERT: B 220 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: B 239 ASN cc_start: 0.7904 (m110) cc_final: 0.7572 (m110) REVERT: B 256 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7790 (mtt180) REVERT: B 277 SER cc_start: 0.8544 (t) cc_final: 0.8163 (p) REVERT: B 289 TYR cc_start: 0.8473 (m-80) cc_final: 0.8229 (m-80) REVERT: N 25 SER cc_start: 0.7982 (OUTLIER) cc_final: 0.7542 (m) outliers start: 30 outliers final: 14 residues processed: 240 average time/residue: 1.3889 time to fit residues: 352.9999 Evaluate side-chains 251 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 133 ARG Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 71 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 0.5980 chunk 85 optimal weight: 0.0270 chunk 12 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.142063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125893 restraints weight = 11494.484| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.94 r_work: 0.3454 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8730 Z= 0.176 Angle : 0.551 19.069 11829 Z= 0.271 Chirality : 0.039 0.142 1331 Planarity : 0.004 0.046 1458 Dihedral : 6.014 82.225 1646 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.02 % Allowed : 17.09 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 1024 helix: 2.66 (0.25), residues: 419 sheet: -0.62 (0.33), residues: 216 loop : -0.64 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 133 HIS 0.005 0.001 HIS A 82 PHE 0.015 0.001 PHE A 74 TYR 0.016 0.001 TYR N 117 ARG 0.006 0.000 ARG A 241 *********************** 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 252 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8271 (mtt) REVERT: R 270 VAL cc_start: 0.7941 (t) cc_final: 0.7578 (p) REVERT: R 331 TYR cc_start: 0.8346 (m-80) cc_final: 0.8132 (m-80) REVERT: R 338 ARG cc_start: 0.7233 (mtt180) cc_final: 0.6960 (mtt180) REVERT: A 24 LYS cc_start: 0.7854 (mmmt) cc_final: 0.7612 (mmmt) REVERT: A 36 VAL cc_start: 0.8369 (p) cc_final: 0.8151 (t) REVERT: A 60 MET cc_start: 0.5870 (ttt) cc_final: 0.5553 (ttt) REVERT: A 77 ASP cc_start: 0.7629 (m-30) cc_final: 0.7260 (m-30) REVERT: A 111 ASP cc_start: 0.7833 (t0) cc_final: 0.7451 (t0) REVERT: A 117 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7959 (mtm110) REVERT: A 151 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7528 (mt-10) REVERT: A 199 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8035 (ttp-170) REVERT: A 200 ILE cc_start: 0.8536 (mt) cc_final: 0.8311 (mm) REVERT: A 202 THR cc_start: 0.7931 (m) cc_final: 0.7537 (p) REVERT: A 208 ARG cc_start: 0.8174 (mtm180) cc_final: 0.7943 (mtm180) REVERT: A 225 ARG cc_start: 0.7873 (tpp-160) cc_final: 0.7490 (mmt-90) REVERT: A 233 ASP cc_start: 0.7718 (m-30) cc_final: 0.7424 (m-30) REVERT: A 244 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7640 (mt-10) REVERT: B 25 CYS cc_start: 0.8158 (m) cc_final: 0.7372 (p) REVERT: B 76 ASP cc_start: 0.7917 (p0) cc_final: 0.7697 (p0) REVERT: B 83 ASP cc_start: 0.8263 (t0) cc_final: 0.7966 (t70) REVERT: B 98 SER cc_start: 0.8103 (m) cc_final: 0.7782 (p) REVERT: B 114 CYS cc_start: 0.7811 (p) cc_final: 0.7519 (p) REVERT: B 153 ASP cc_start: 0.7681 (p0) cc_final: 0.7435 (p0) REVERT: B 160 SER cc_start: 0.8169 (t) cc_final: 0.7825 (p) REVERT: B 161 SER cc_start: 0.8422 (t) cc_final: 0.8104 (m) REVERT: B 195 ASP cc_start: 0.7692 (p0) cc_final: 0.7446 (p0) REVERT: B 197 ARG cc_start: 0.7912 (mmt180) cc_final: 0.7373 (mtt180) REVERT: B 219 ARG cc_start: 0.8235 (mtp85) cc_final: 0.8010 (ttm-80) REVERT: B 220 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: B 230 ASN cc_start: 0.8258 (m-40) cc_final: 0.7727 (m-40) REVERT: B 239 ASN cc_start: 0.7926 (m110) cc_final: 0.7662 (m110) REVERT: B 258 ASP cc_start: 0.7583 (t0) cc_final: 0.7154 (t0) REVERT: B 259 GLN cc_start: 0.8346 (pt0) cc_final: 0.7328 (pt0) REVERT: B 277 SER cc_start: 0.8506 (t) cc_final: 0.8147 (p) REVERT: B 289 TYR cc_start: 0.8397 (m-80) cc_final: 0.8158 (m-80) REVERT: N 25 SER cc_start: 0.7894 (t) cc_final: 0.7550 (m) outliers start: 27 outliers final: 14 residues processed: 231 average time/residue: 1.2185 time to fit residues: 299.0803 Evaluate side-chains 240 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 196 ILE Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 71 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 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 239 ASN ** B 295 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 = 0.3787 r_free = 0.3787 target = 0.139992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123535 restraints weight = 11565.972| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.95 r_work: 0.3408 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8730 Z= 0.275 Angle : 0.578 19.873 11829 Z= 0.284 Chirality : 0.041 0.145 1331 Planarity : 0.004 0.047 1458 Dihedral : 6.047 82.189 1646 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.91 % Allowed : 17.77 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1024 helix: 2.54 (0.25), residues: 419 sheet: -0.60 (0.33), residues: 216 loop : -0.65 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 133 HIS 0.005 0.001 HIS A 82 PHE 0.017 0.002 PHE N 68 TYR 0.017 0.002 TYR N 117 ARG 0.005 0.000 ARG A 241 *********************** 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: 26 poor density : 227 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8243 (mtt) REVERT: R 270 VAL cc_start: 0.8017 (t) cc_final: 0.7648 (p) REVERT: R 331 TYR cc_start: 0.8398 (m-80) cc_final: 0.8132 (m-80) REVERT: R 338 ARG cc_start: 0.7282 (mtt180) cc_final: 0.7008 (mtt180) REVERT: A 24 LYS cc_start: 0.7860 (mmmt) cc_final: 0.7634 (mmmt) REVERT: A 36 VAL cc_start: 0.8380 (p) cc_final: 0.8175 (t) REVERT: A 60 MET cc_start: 0.5839 (ttt) cc_final: 0.5540 (ttt) REVERT: A 77 ASP cc_start: 0.7670 (m-30) cc_final: 0.7326 (m-30) REVERT: A 111 ASP cc_start: 0.7823 (t0) cc_final: 0.7467 (t0) REVERT: A 117 ARG cc_start: 0.8256 (mtp85) cc_final: 0.8056 (mtm110) REVERT: A 132 ARG cc_start: 0.7805 (ttt180) cc_final: 0.7603 (ttt180) REVERT: A 146 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7562 (mm-40) REVERT: A 151 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7519 (mt-10) REVERT: A 199 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8040 (ttp-170) REVERT: A 202 THR cc_start: 0.7956 (m) cc_final: 0.7591 (p) REVERT: A 208 ARG cc_start: 0.8231 (mtm180) cc_final: 0.7983 (mtm180) REVERT: A 225 ARG cc_start: 0.7928 (tpp-160) cc_final: 0.7660 (mmt-90) REVERT: A 233 ASP cc_start: 0.7736 (m-30) cc_final: 0.7457 (m-30) REVERT: A 244 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7841 (mt-10) REVERT: B 20 ASP cc_start: 0.7316 (m-30) cc_final: 0.6901 (m-30) REVERT: B 25 CYS cc_start: 0.8163 (m) cc_final: 0.7365 (p) REVERT: B 98 SER cc_start: 0.8177 (m) cc_final: 0.7859 (p) REVERT: B 114 CYS cc_start: 0.7824 (p) cc_final: 0.7566 (p) REVERT: B 153 ASP cc_start: 0.7679 (p0) cc_final: 0.7437 (p0) REVERT: B 160 SER cc_start: 0.8156 (t) cc_final: 0.7825 (p) REVERT: B 161 SER cc_start: 0.8480 (t) cc_final: 0.8125 (m) REVERT: B 195 ASP cc_start: 0.7724 (p0) cc_final: 0.7477 (p0) REVERT: B 197 ARG cc_start: 0.7937 (mmt180) cc_final: 0.7421 (mtt180) REVERT: B 219 ARG cc_start: 0.8271 (mtp85) cc_final: 0.8039 (ttm-80) REVERT: B 220 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: B 230 ASN cc_start: 0.8241 (m-40) cc_final: 0.7719 (m-40) REVERT: B 239 ASN cc_start: 0.7967 (m-40) cc_final: 0.7602 (m110) REVERT: B 256 ARG cc_start: 0.8197 (mtt180) cc_final: 0.7873 (mtt180) REVERT: B 277 SER cc_start: 0.8522 (t) cc_final: 0.8154 (p) REVERT: B 289 TYR cc_start: 0.8444 (m-80) cc_final: 0.8175 (m-80) REVERT: N 25 SER cc_start: 0.8033 (t) cc_final: 0.7595 (m) outliers start: 26 outliers final: 15 residues processed: 236 average time/residue: 1.2911 time to fit residues: 322.2101 Evaluate side-chains 245 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 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 75 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 49 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 75 GLN B 110 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124510 restraints weight = 11525.407| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.94 r_work: 0.3429 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8730 Z= 0.211 Angle : 0.575 20.434 11829 Z= 0.280 Chirality : 0.040 0.144 1331 Planarity : 0.004 0.050 1458 Dihedral : 5.956 80.968 1646 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.91 % Allowed : 18.10 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 1024 helix: 2.56 (0.25), residues: 419 sheet: -0.58 (0.33), residues: 221 loop : -0.60 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 133 HIS 0.006 0.001 HIS A 82 PHE 0.012 0.001 PHE B 199 TYR 0.017 0.001 TYR N 117 ARG 0.005 0.000 ARG A 241 *********************** 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 253 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8237 (mtt) REVERT: R 270 VAL cc_start: 0.8011 (t) cc_final: 0.7644 (p) REVERT: R 331 TYR cc_start: 0.8393 (m-80) cc_final: 0.8148 (m-80) REVERT: R 338 ARG cc_start: 0.7283 (mtt180) cc_final: 0.7005 (mtt180) REVERT: A 24 LYS cc_start: 0.7859 (mmmt) cc_final: 0.7636 (mmmt) REVERT: A 36 VAL cc_start: 0.8363 (p) cc_final: 0.8156 (t) REVERT: A 60 MET cc_start: 0.5857 (ttt) cc_final: 0.5546 (ttt) REVERT: A 77 ASP cc_start: 0.7653 (m-30) cc_final: 0.7311 (m-30) REVERT: A 111 ASP cc_start: 0.7826 (t0) cc_final: 0.7460 (t0) REVERT: A 135 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7584 (mtm-85) REVERT: A 151 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7557 (mt-10) REVERT: A 199 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8032 (ttp-170) REVERT: A 202 THR cc_start: 0.7940 (m) cc_final: 0.7548 (p) REVERT: A 208 ARG cc_start: 0.8205 (mtm180) cc_final: 0.7665 (mtm180) REVERT: A 225 ARG cc_start: 0.7933 (tpp-160) cc_final: 0.7655 (mmt-90) REVERT: A 233 ASP cc_start: 0.7732 (m-30) cc_final: 0.7457 (m-30) REVERT: A 244 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 20 ASP cc_start: 0.7291 (m-30) cc_final: 0.6886 (m-30) REVERT: B 25 CYS cc_start: 0.8154 (m) cc_final: 0.7377 (p) REVERT: B 98 SER cc_start: 0.8146 (m) cc_final: 0.7831 (p) REVERT: B 114 CYS cc_start: 0.7790 (p) cc_final: 0.7540 (p) REVERT: B 160 SER cc_start: 0.8175 (t) cc_final: 0.7830 (p) REVERT: B 161 SER cc_start: 0.8473 (t) cc_final: 0.8118 (m) REVERT: B 195 ASP cc_start: 0.7725 (p0) cc_final: 0.7478 (p0) REVERT: B 197 ARG cc_start: 0.7928 (mmt180) cc_final: 0.7412 (mtt180) REVERT: B 219 ARG cc_start: 0.8233 (mtp85) cc_final: 0.8006 (ttm-80) REVERT: B 228 ASP cc_start: 0.7750 (m-30) cc_final: 0.7350 (m-30) REVERT: B 230 ASN cc_start: 0.8250 (m-40) cc_final: 0.7729 (m-40) REVERT: B 239 ASN cc_start: 0.7955 (m-40) cc_final: 0.7617 (m110) REVERT: B 256 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7857 (mtt180) REVERT: B 259 GLN cc_start: 0.8386 (pt0) cc_final: 0.7446 (pt0) REVERT: B 277 SER cc_start: 0.8507 (t) cc_final: 0.8140 (p) REVERT: B 289 TYR cc_start: 0.8406 (m-80) cc_final: 0.8104 (m-80) REVERT: N 25 SER cc_start: 0.7997 (OUTLIER) cc_final: 0.7585 (m) outliers start: 26 outliers final: 17 residues processed: 235 average time/residue: 1.2890 time to fit residues: 321.2216 Evaluate side-chains 245 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 333 PHE Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 75 GLN 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 37 ILE Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 160 GLN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 75 GLN B 110 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124815 restraints weight = 11368.446| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.92 r_work: 0.3439 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8730 Z= 0.215 Angle : 0.578 20.397 11829 Z= 0.281 Chirality : 0.040 0.144 1331 Planarity : 0.004 0.049 1458 Dihedral : 5.916 80.231 1646 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.12 % Allowed : 19.78 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 1024 helix: 2.54 (0.25), residues: 419 sheet: -0.64 (0.33), residues: 221 loop : -0.59 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 133 HIS 0.005 0.001 HIS A 82 PHE 0.014 0.001 PHE A 74 TYR 0.025 0.001 TYR N 60 ARG 0.004 0.000 ARG A 241 ********************** 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 247 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8312 (mtt) REVERT: R 270 VAL cc_start: 0.7993 (t) cc_final: 0.7623 (p) REVERT: R 331 TYR cc_start: 0.8398 (m-80) cc_final: 0.8155 (m-80) REVERT: R 338 ARG cc_start: 0.7290 (mtt180) cc_final: 0.7015 (mtt180) REVERT: A 24 LYS cc_start: 0.7843 (mmmt) cc_final: 0.7617 (mmmt) REVERT: A 36 VAL cc_start: 0.8369 (p) cc_final: 0.8150 (t) REVERT: A 60 MET cc_start: 0.5863 (ttt) cc_final: 0.5553 (ttt) REVERT: A 77 ASP cc_start: 0.7674 (m-30) cc_final: 0.7203 (m-30) REVERT: A 111 ASP cc_start: 0.7814 (t0) cc_final: 0.7444 (t0) REVERT: A 169 ARG cc_start: 0.7992 (ptp-170) cc_final: 0.7718 (mtm-85) REVERT: A 202 THR cc_start: 0.7905 (m) cc_final: 0.7514 (p) REVERT: A 208 ARG cc_start: 0.8174 (mtm180) cc_final: 0.7937 (mtm180) REVERT: A 233 ASP cc_start: 0.7717 (m-30) cc_final: 0.7435 (m-30) REVERT: A 244 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 20 ASP cc_start: 0.7268 (m-30) cc_final: 0.6871 (m-30) REVERT: B 25 CYS cc_start: 0.8156 (m) cc_final: 0.7383 (p) REVERT: B 98 SER cc_start: 0.8144 (m) cc_final: 0.7824 (p) REVERT: B 114 CYS cc_start: 0.7793 (p) cc_final: 0.7545 (p) REVERT: B 160 SER cc_start: 0.8150 (t) cc_final: 0.7830 (p) REVERT: B 195 ASP cc_start: 0.7713 (p0) cc_final: 0.7466 (p0) REVERT: B 197 ARG cc_start: 0.7906 (mmt180) cc_final: 0.7404 (mtt180) REVERT: B 219 ARG cc_start: 0.8229 (mtp85) cc_final: 0.8008 (ttm-80) REVERT: B 220 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: B 228 ASP cc_start: 0.7745 (m-30) cc_final: 0.7340 (m-30) REVERT: B 230 ASN cc_start: 0.8242 (m-40) cc_final: 0.7710 (m-40) REVERT: B 239 ASN cc_start: 0.7978 (m-40) cc_final: 0.7647 (m110) REVERT: B 256 ARG cc_start: 0.8166 (mtt180) cc_final: 0.7834 (mtt180) REVERT: B 258 ASP cc_start: 0.7498 (t0) cc_final: 0.7223 (t0) REVERT: B 259 GLN cc_start: 0.8367 (pt0) cc_final: 0.7439 (pt0) REVERT: B 277 SER cc_start: 0.8480 (t) cc_final: 0.8123 (p) REVERT: B 283 ARG cc_start: 0.8486 (tpp80) cc_final: 0.8143 (tpt-90) REVERT: B 289 TYR cc_start: 0.8349 (m-80) cc_final: 0.8071 (m-80) REVERT: N 25 SER cc_start: 0.7969 (t) cc_final: 0.7627 (m) outliers start: 19 outliers final: 14 residues processed: 236 average time/residue: 1.7230 time to fit residues: 429.4376 Evaluate side-chains 234 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 333 PHE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 99 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 72 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 75 GLN B 110 ASN B 220 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123145 restraints weight = 11560.236| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.94 r_work: 0.3437 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8730 Z= 0.216 Angle : 0.586 20.156 11829 Z= 0.286 Chirality : 0.040 0.155 1331 Planarity : 0.004 0.049 1458 Dihedral : 5.898 79.734 1646 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.01 % Allowed : 20.34 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.27), residues: 1024 helix: 2.52 (0.25), residues: 419 sheet: -0.70 (0.33), residues: 221 loop : -0.59 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 133 HIS 0.004 0.001 HIS A 82 PHE 0.014 0.001 PHE A 74 TYR 0.017 0.001 TYR N 117 ARG 0.005 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7690.44 seconds wall clock time: 133 minutes 8.99 seconds (7988.99 seconds total)