Starting phenix.real_space_refine on Thu Feb 13 07:59:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8okx_16933/02_2025/8okx_16933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8okx_16933/02_2025/8okx_16933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8okx_16933/02_2025/8okx_16933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8okx_16933/02_2025/8okx_16933.map" model { file = "/net/cci-nas-00/data/ceres_data/8okx_16933/02_2025/8okx_16933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8okx_16933/02_2025/8okx_16933.cif" } resolution = 3.51 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= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2959 atoms to isotropic. 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 Zn 1 6.06 5 S 43 5.16 5 C 4061 2.51 5 N 1093 2.21 5 O 1201 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6399 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2966 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "B" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1737 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain: "C" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 873 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "D" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1884 SG CYS A 396 23.491 48.998 82.872 1.00 91.65 S ATOM 1890 SG CYS A 397 21.155 46.114 82.380 1.00 90.83 S ATOM 1949 SG CYS A 404 24.813 45.618 81.419 1.00 64.49 S Time building chain proxies: 4.45, per 1000 atoms: 0.70 Number of scatterers: 6399 At special positions: 0 Unit cell: (103.976, 96.368, 138.212, 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) Zn 1 29.99 S 43 16.00 O 1201 8.00 N 1093 7.00 C 4061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.34 Conformation dependent library (CDL) restraints added in 931.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 390 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 397 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 396 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 404 " Number of angles added : 3 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 33.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 161 through 174 removed outlier: 4.102A pdb=" N LEU A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 200 removed outlier: 3.653A pdb=" N THR A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N MET A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 removed outlier: 4.229A pdb=" N ASN A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 340 through 353 removed outlier: 7.702A pdb=" N ALA A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N LYS A 347 " --> pdb=" O TRP A 343 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.592A pdb=" N LEU A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.840A pdb=" N LYS A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET A 413 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 449 removed outlier: 4.052A pdb=" N VAL A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.192A pdb=" N ASP A 456 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 Processing helix chain 'A' and resid 497 through 514 Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.636A pdb=" N PHE A 522 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.917A pdb=" N TYR B 178 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 289 removed outlier: 4.711A pdb=" N CYS B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 319 removed outlier: 7.617A pdb=" N TRP B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 39 removed outlier: 4.080A pdb=" N SER C 39 " --> pdb=" O HIS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 47 removed outlier: 3.557A pdb=" N SER C 47 " --> pdb=" O LYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 83 Processing helix chain 'C' and resid 103 through 111 removed outlier: 3.760A pdb=" N ALA C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 36 Processing helix chain 'D' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.752A pdb=" N LYS A 231 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 322 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 240 " --> pdb=" O PHE A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.752A pdb=" N LYS A 231 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 308 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 309 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 112 removed outlier: 5.579A pdb=" N ARG B 139 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N LEU B 110 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N ALA B 137 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 256 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 119 removed outlier: 3.948A pdb=" N SER B 263 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL B 267 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 154 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG B 269 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 152 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 149 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP B 151 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 231 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL B 242 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N PHE B 233 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 240 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 32 removed outlier: 3.648A pdb=" N VAL C 31 " --> pdb=" O VAL C 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 12 through 16 removed outlier: 6.594A pdb=" N MET D 6 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU D 77 " --> pdb=" O MET D 6 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG D 8 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N PHE D 79 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 12 through 16 removed outlier: 6.594A pdb=" N MET D 6 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU D 77 " --> pdb=" O MET D 6 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG D 8 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N PHE D 79 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG D 68 " --> pdb=" O ALA D 71 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 732 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: 2.03 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.23: 18 1.23 - 1.41: 2634 1.41 - 1.59: 3818 1.59 - 1.77: 2 1.77 - 1.95: 63 Bond restraints: 6535 Sorted by residual: bond pdb=" CG PRO D 39 " pdb=" CD PRO D 39 " ideal model delta sigma weight residual 1.503 1.044 0.459 3.40e-02 8.65e+02 1.82e+02 bond pdb=" SD MET A 298 " pdb=" CE MET A 298 " ideal model delta sigma weight residual 1.791 1.950 -0.159 2.50e-02 1.60e+03 4.06e+01 bond pdb=" SD MET A 413 " pdb=" CE MET A 413 " ideal model delta sigma weight residual 1.791 1.950 -0.159 2.50e-02 1.60e+03 4.03e+01 bond pdb=" SD MET A 185 " pdb=" CE MET A 185 " ideal model delta sigma weight residual 1.791 1.949 -0.158 2.50e-02 1.60e+03 4.02e+01 bond pdb=" SD MET A 276 " pdb=" CE MET A 276 " ideal model delta sigma weight residual 1.791 1.949 -0.158 2.50e-02 1.60e+03 4.02e+01 ... (remaining 6530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 8745 4.35 - 8.70: 50 8.70 - 13.05: 3 13.05 - 17.40: 2 17.40 - 21.75: 1 Bond angle restraints: 8801 Sorted by residual: angle pdb=" N PRO D 39 " pdb=" CD PRO D 39 " pdb=" CG PRO D 39 " ideal model delta sigma weight residual 103.20 81.45 21.75 1.50e+00 4.44e-01 2.10e+02 angle pdb=" CA PRO D 39 " pdb=" N PRO D 39 " pdb=" CD PRO D 39 " ideal model delta sigma weight residual 112.00 95.64 16.36 1.40e+00 5.10e-01 1.37e+02 angle pdb=" CA PRO D 39 " pdb=" CB PRO D 39 " pdb=" CG PRO D 39 " ideal model delta sigma weight residual 104.50 89.18 15.32 1.90e+00 2.77e-01 6.50e+01 angle pdb=" CA PRO C 97 " pdb=" N PRO C 97 " pdb=" CD PRO C 97 " ideal model delta sigma weight residual 112.00 103.77 8.23 1.40e+00 5.10e-01 3.46e+01 angle pdb=" N PRO D 39 " pdb=" CA PRO D 39 " pdb=" CB PRO D 39 " ideal model delta sigma weight residual 103.26 97.14 6.12 1.14e+00 7.69e-01 2.88e+01 ... (remaining 8796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 3462 17.38 - 34.75: 393 34.75 - 52.13: 78 52.13 - 69.50: 25 69.50 - 86.88: 8 Dihedral angle restraints: 3966 sinusoidal: 1643 harmonic: 2323 Sorted by residual: dihedral pdb=" CA GLU B 130 " pdb=" C GLU B 130 " pdb=" N TYR B 131 " pdb=" CA TYR B 131 " ideal model delta harmonic sigma weight residual -180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA VAL D 102 " pdb=" C VAL D 102 " pdb=" N MET D 103 " pdb=" CA MET D 103 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER A 213 " pdb=" C SER A 213 " pdb=" N TYR A 214 " pdb=" CA TYR A 214 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 3963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 775 0.057 - 0.115: 151 0.115 - 0.172: 24 0.172 - 0.229: 3 0.229 - 0.287: 5 Chirality restraints: 958 Sorted by residual: chirality pdb=" CA ASN B 122 " pdb=" N ASN B 122 " pdb=" C ASN B 122 " pdb=" CB ASN B 122 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA SER B 132 " pdb=" N SER B 132 " pdb=" C SER B 132 " pdb=" CB SER B 132 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO C 97 " pdb=" N PRO C 97 " pdb=" C PRO C 97 " pdb=" CB PRO C 97 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 955 not shown) Planarity restraints: 1127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 510 " 0.074 2.00e-02 2.50e+03 4.61e-02 4.26e+01 pdb=" CG TYR A 510 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 510 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 510 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 510 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 510 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 510 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 510 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 38 " -0.110 5.00e-02 4.00e+02 1.50e-01 3.58e+01 pdb=" N PRO D 39 " 0.258 5.00e-02 4.00e+02 pdb=" CA PRO D 39 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO D 39 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 128 " 0.060 2.00e-02 2.50e+03 4.47e-02 2.99e+01 pdb=" CG HIS B 128 " -0.071 2.00e-02 2.50e+03 pdb=" ND1 HIS B 128 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS B 128 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 HIS B 128 " 0.029 2.00e-02 2.50e+03 pdb=" NE2 HIS B 128 " 0.034 2.00e-02 2.50e+03 ... (remaining 1124 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 27 2.47 - 3.07: 4344 3.07 - 3.68: 9749 3.68 - 4.29: 13163 4.29 - 4.90: 21836 Nonbonded interactions: 49119 Sorted by model distance: nonbonded pdb=" CE LYS A 171 " pdb=" CE1 PHE A 522 " model vdw 1.857 3.740 nonbonded pdb=" CE LYS A 171 " pdb=" CD1 PHE A 522 " model vdw 1.944 3.740 nonbonded pdb=" OD2 ASP A 465 " pdb=" NH2 ARG A 512 " model vdw 2.208 3.120 nonbonded pdb=" OH TYR C 79 " pdb=" O PRO C 91 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASP D 40 " pdb=" NH2 ARG D 80 " model vdw 2.254 3.120 ... (remaining 49114 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 group one per residue 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.580 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.459 6535 Z= 0.661 Angle : 0.988 21.749 8801 Z= 0.581 Chirality : 0.051 0.287 958 Planarity : 0.009 0.150 1127 Dihedral : 16.065 86.877 2462 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.32 % Favored : 93.17 % Rotamer: Outliers : 0.42 % Allowed : 19.55 % Favored : 80.03 % 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: -1.03 (0.30), residues: 791 helix: -0.16 (0.33), residues: 247 sheet: -0.35 (0.47), residues: 124 loop : -1.06 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 107 HIS 0.010 0.002 HIS B 283 PHE 0.044 0.002 PHE B 127 TYR 0.085 0.004 TYR A 510 ARG 0.007 0.001 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 MET cc_start: -0.2069 (ttm) cc_final: -0.2326 (mmm) REVERT: C 77 PHE cc_start: 0.7584 (m-10) cc_final: 0.7209 (m-10) outliers start: 3 outliers final: 0 residues processed: 97 average time/residue: 0.2397 time to fit residues: 29.4161 Evaluate side-chains 69 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.0570 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.090173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.064942 restraints weight = 51459.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.065425 restraints weight = 36381.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.065290 restraints weight = 26307.437| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6535 Z= 0.252 Angle : 0.742 12.064 8801 Z= 0.375 Chirality : 0.044 0.188 958 Planarity : 0.007 0.133 1127 Dihedral : 5.289 61.737 862 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.31 % Favored : 94.56 % Rotamer: Outliers : 2.53 % Allowed : 20.82 % Favored : 76.65 % 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: -0.77 (0.30), residues: 791 helix: 0.34 (0.34), residues: 241 sheet: -0.35 (0.47), residues: 131 loop : -1.04 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 193 HIS 0.020 0.002 HIS B 283 PHE 0.019 0.001 PHE B 210 TYR 0.016 0.001 TYR C 18 ARG 0.015 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 MET cc_start: 0.7945 (mmm) cc_final: 0.7723 (mmt) REVERT: B 227 TRP cc_start: 0.8170 (t-100) cc_final: 0.7630 (t-100) REVERT: B 255 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7620 (mmt) outliers start: 18 outliers final: 8 residues processed: 90 average time/residue: 0.2041 time to fit residues: 24.1383 Evaluate side-chains 76 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 ASN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.080678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.056061 restraints weight = 55379.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.056333 restraints weight = 36318.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.056333 restraints weight = 25577.093| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 6535 Z= 0.519 Angle : 0.902 11.775 8801 Z= 0.465 Chirality : 0.048 0.177 958 Planarity : 0.007 0.091 1127 Dihedral : 6.158 75.086 862 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.83 % Favored : 92.92 % Rotamer: Outliers : 4.50 % Allowed : 22.22 % Favored : 73.28 % 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: -1.53 (0.28), residues: 791 helix: -0.61 (0.31), residues: 242 sheet: -0.38 (0.47), residues: 128 loop : -1.44 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 193 HIS 0.021 0.003 HIS B 283 PHE 0.020 0.003 PHE A 379 TYR 0.017 0.002 TYR C 18 ARG 0.005 0.001 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 MET cc_start: 0.8255 (mmm) cc_final: 0.7979 (mmm) REVERT: B 227 TRP cc_start: 0.8249 (t-100) cc_final: 0.7929 (t-100) REVERT: C 75 MET cc_start: 0.9300 (tpp) cc_final: 0.8929 (tpp) REVERT: C 80 LYS cc_start: 0.9721 (tppt) cc_final: 0.9318 (pttm) REVERT: C 83 TYR cc_start: 0.8962 (m-80) cc_final: 0.6766 (m-80) REVERT: D 4 PHE cc_start: 0.9277 (t80) cc_final: 0.8747 (t80) outliers start: 32 outliers final: 19 residues processed: 91 average time/residue: 0.2103 time to fit residues: 25.0216 Evaluate side-chains 82 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 40.0000 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.087646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.063038 restraints weight = 52576.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.062590 restraints weight = 36090.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.062590 restraints weight = 26019.726| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6535 Z= 0.275 Angle : 0.757 12.954 8801 Z= 0.380 Chirality : 0.044 0.149 958 Planarity : 0.005 0.067 1127 Dihedral : 5.888 75.940 862 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.52 % Allowed : 23.49 % Favored : 73.00 % 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: -1.24 (0.29), residues: 791 helix: -0.23 (0.32), residues: 249 sheet: -0.65 (0.46), residues: 130 loop : -1.21 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 193 HIS 0.020 0.002 HIS B 283 PHE 0.014 0.002 PHE A 280 TYR 0.017 0.001 TYR D 45 ARG 0.014 0.001 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7442 (mmmt) REVERT: B 164 MET cc_start: 0.8194 (mmm) cc_final: 0.7900 (mmm) REVERT: B 227 TRP cc_start: 0.8325 (t-100) cc_final: 0.7912 (t-100) REVERT: B 265 MET cc_start: 0.8157 (mmm) cc_final: 0.7568 (mmm) REVERT: C 80 LYS cc_start: 0.9772 (tppt) cc_final: 0.9308 (pttp) REVERT: C 83 TYR cc_start: 0.7965 (m-80) cc_final: 0.6997 (m-80) REVERT: D 6 MET cc_start: 0.6016 (tpp) cc_final: 0.5802 (tpp) REVERT: D 35 LEU cc_start: 0.6887 (tp) cc_final: 0.6583 (pt) outliers start: 25 outliers final: 14 residues processed: 86 average time/residue: 0.2421 time to fit residues: 26.6004 Evaluate side-chains 82 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 62 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 0.0170 chunk 8 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.087098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.060608 restraints weight = 51182.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.060508 restraints weight = 37772.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.060553 restraints weight = 27071.188| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6535 Z= 0.408 Angle : 0.827 10.210 8801 Z= 0.424 Chirality : 0.046 0.222 958 Planarity : 0.006 0.097 1127 Dihedral : 6.249 80.949 862 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 5.49 % Allowed : 23.07 % Favored : 71.45 % 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: -1.57 (0.28), residues: 791 helix: -0.40 (0.32), residues: 244 sheet: -0.79 (0.44), residues: 127 loop : -1.50 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 193 HIS 0.018 0.002 HIS B 283 PHE 0.017 0.002 PHE A 503 TYR 0.016 0.002 TYR C 18 ARG 0.010 0.001 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 71 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7537 (mmmt) REVERT: B 164 MET cc_start: 0.8219 (mmm) cc_final: 0.7933 (mmm) REVERT: B 227 TRP cc_start: 0.8288 (t-100) cc_final: 0.7773 (t-100) REVERT: B 265 MET cc_start: 0.8131 (mmm) cc_final: 0.7642 (tpt) REVERT: C 75 MET cc_start: 0.8803 (tpp) cc_final: 0.8595 (tpt) REVERT: C 83 TYR cc_start: 0.7911 (m-80) cc_final: 0.7510 (m-10) REVERT: C 90 ILE cc_start: 0.5316 (tp) cc_final: 0.4212 (tp) outliers start: 39 outliers final: 26 residues processed: 99 average time/residue: 0.2083 time to fit residues: 26.9501 Evaluate side-chains 90 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 52 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 13 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 74 optimal weight: 0.0370 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.080237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.055476 restraints weight = 54790.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.055832 restraints weight = 36303.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.055831 restraints weight = 24865.238| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6535 Z= 0.177 Angle : 0.756 14.507 8801 Z= 0.368 Chirality : 0.044 0.210 958 Planarity : 0.004 0.059 1127 Dihedral : 5.696 76.347 862 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.81 % Allowed : 25.32 % Favored : 71.87 % 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 (0.30), residues: 791 helix: 0.07 (0.33), residues: 248 sheet: -0.61 (0.44), residues: 134 loop : -1.19 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 455 HIS 0.016 0.001 HIS B 283 PHE 0.010 0.001 PHE A 280 TYR 0.013 0.001 TYR C 79 ARG 0.005 0.001 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7570 (mmmt) REVERT: B 164 MET cc_start: 0.8194 (mmm) cc_final: 0.7879 (mmm) REVERT: B 227 TRP cc_start: 0.8459 (t-100) cc_final: 0.7997 (t-100) REVERT: B 265 MET cc_start: 0.8618 (mmm) cc_final: 0.8380 (tpt) REVERT: B 286 ARG cc_start: 0.8375 (tpt170) cc_final: 0.8108 (tpp-160) REVERT: C 83 TYR cc_start: 0.7976 (m-80) cc_final: 0.7491 (m-10) REVERT: C 90 ILE cc_start: 0.4794 (tp) cc_final: 0.3500 (tp) REVERT: D 49 GLN cc_start: 0.7455 (mp10) cc_final: 0.7252 (pm20) outliers start: 20 outliers final: 12 residues processed: 85 average time/residue: 0.2201 time to fit residues: 24.1861 Evaluate side-chains 78 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain D residue 13 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 40.0000 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.088112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.062340 restraints weight = 52322.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.062273 restraints weight = 35396.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.062293 restraints weight = 26603.312| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6535 Z= 0.173 Angle : 0.753 13.356 8801 Z= 0.363 Chirality : 0.043 0.232 958 Planarity : 0.004 0.059 1127 Dihedral : 5.496 72.672 862 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.95 % Allowed : 26.02 % Favored : 71.03 % 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: -0.84 (0.30), residues: 791 helix: 0.22 (0.33), residues: 248 sheet: -0.50 (0.44), residues: 127 loop : -1.02 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 105 HIS 0.014 0.001 HIS B 283 PHE 0.024 0.001 PHE C 109 TYR 0.015 0.001 TYR C 18 ARG 0.005 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7589 (mmmt) REVERT: A 400 LYS cc_start: 0.9068 (tppt) cc_final: 0.8840 (tptp) REVERT: B 163 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8519 (p0) REVERT: B 164 MET cc_start: 0.8195 (mmm) cc_final: 0.7944 (mmt) REVERT: B 227 TRP cc_start: 0.8335 (t-100) cc_final: 0.7886 (t-100) REVERT: C 90 ILE cc_start: 0.3747 (tp) cc_final: 0.2704 (tp) outliers start: 21 outliers final: 12 residues processed: 86 average time/residue: 0.2238 time to fit residues: 25.0832 Evaluate side-chains 77 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain D residue 4 PHE Chi-restraints excluded: chain D residue 13 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.080477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.056051 restraints weight = 55735.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.056067 restraints weight = 37861.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.056067 restraints weight = 27261.819| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6535 Z= 0.332 Angle : 0.826 14.589 8801 Z= 0.407 Chirality : 0.046 0.260 958 Planarity : 0.005 0.058 1127 Dihedral : 5.816 74.442 862 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.66 % Allowed : 25.74 % Favored : 70.60 % 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: -1.11 (0.29), residues: 791 helix: 0.01 (0.33), residues: 249 sheet: -0.70 (0.41), residues: 140 loop : -1.18 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 193 HIS 0.013 0.002 HIS B 283 PHE 0.018 0.002 PHE A 280 TYR 0.017 0.002 TYR C 18 ARG 0.006 0.001 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7575 (mmmt) REVERT: B 164 MET cc_start: 0.8118 (mmm) cc_final: 0.7770 (mmp) REVERT: B 227 TRP cc_start: 0.8626 (t-100) cc_final: 0.7959 (t-100) REVERT: C 83 TYR cc_start: 0.8387 (m-10) cc_final: 0.7874 (m-10) REVERT: C 90 ILE cc_start: 0.5437 (tp) cc_final: 0.3880 (tp) outliers start: 26 outliers final: 19 residues processed: 85 average time/residue: 0.2103 time to fit residues: 23.4956 Evaluate side-chains 85 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain D residue 4 PHE Chi-restraints excluded: chain D residue 13 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.0050 chunk 50 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN A 449 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.080839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.056551 restraints weight = 56407.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.056659 restraints weight = 36844.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.056659 restraints weight = 26374.468| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6535 Z= 0.192 Angle : 0.820 15.644 8801 Z= 0.390 Chirality : 0.045 0.202 958 Planarity : 0.004 0.058 1127 Dihedral : 5.578 69.724 862 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.53 % Allowed : 27.14 % Favored : 70.32 % 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: -0.88 (0.30), residues: 791 helix: 0.24 (0.34), residues: 249 sheet: -0.68 (0.42), residues: 133 loop : -1.02 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 455 HIS 0.013 0.001 HIS B 283 PHE 0.015 0.001 PHE C 109 TYR 0.017 0.001 TYR C 18 ARG 0.004 0.000 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7502 (mmmt) REVERT: B 164 MET cc_start: 0.7963 (mmm) cc_final: 0.7624 (mmt) REVERT: B 227 TRP cc_start: 0.8627 (t-100) cc_final: 0.7928 (t-100) REVERT: B 319 MET cc_start: 0.2315 (ttt) cc_final: 0.1696 (tpp) REVERT: C 83 TYR cc_start: 0.8491 (m-10) cc_final: 0.7956 (m-10) REVERT: C 90 ILE cc_start: 0.5328 (tp) cc_final: 0.3730 (tp) outliers start: 18 outliers final: 16 residues processed: 76 average time/residue: 0.2212 time to fit residues: 21.8744 Evaluate side-chains 81 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain D residue 4 PHE Chi-restraints excluded: chain D residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 0.0000 chunk 56 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 overall best weight: 2.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.080004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.055869 restraints weight = 56223.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.055973 restraints weight = 35407.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.056454 restraints weight = 24142.708| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6535 Z= 0.279 Angle : 0.832 13.142 8801 Z= 0.403 Chirality : 0.045 0.204 958 Planarity : 0.005 0.060 1127 Dihedral : 5.715 68.342 862 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.39 % Allowed : 27.14 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.05 (0.29), residues: 791 helix: 0.09 (0.33), residues: 250 sheet: -0.69 (0.42), residues: 127 loop : -1.15 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 227 HIS 0.013 0.001 HIS B 283 PHE 0.015 0.002 PHE C 109 TYR 0.017 0.001 TYR C 18 ARG 0.005 0.001 ARG D 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7576 (mmmt) REVERT: B 164 MET cc_start: 0.7969 (mmm) cc_final: 0.7626 (mmm) REVERT: B 227 TRP cc_start: 0.8618 (t-100) cc_final: 0.7930 (t-100) REVERT: B 319 MET cc_start: 0.2621 (ttt) cc_final: 0.1809 (tpp) REVERT: C 83 TYR cc_start: 0.8630 (m-10) cc_final: 0.8077 (m-10) REVERT: C 90 ILE cc_start: 0.5691 (tp) cc_final: 0.4045 (tp) outliers start: 17 outliers final: 15 residues processed: 79 average time/residue: 0.2321 time to fit residues: 23.6520 Evaluate side-chains 82 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain D residue 4 PHE Chi-restraints excluded: chain D residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 54 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.079887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.055684 restraints weight = 58106.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.055813 restraints weight = 36045.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.055835 restraints weight = 26879.239| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6535 Z= 0.271 Angle : 0.841 15.667 8801 Z= 0.407 Chirality : 0.046 0.185 958 Planarity : 0.005 0.057 1127 Dihedral : 5.772 64.385 862 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.53 % Allowed : 26.86 % Favored : 70.60 % 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: -1.13 (0.29), residues: 791 helix: 0.01 (0.33), residues: 250 sheet: -0.74 (0.43), residues: 127 loop : -1.19 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 227 HIS 0.013 0.001 HIS B 283 PHE 0.036 0.002 PHE C 109 TYR 0.019 0.001 TYR C 18 ARG 0.009 0.001 ARG D 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3144.40 seconds wall clock time: 56 minutes 38.66 seconds (3398.66 seconds total)