Starting phenix.real_space_refine on Thu Mar 13 10:13:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8okx_16933/03_2025/8okx_16933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8okx_16933/03_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_16933/03_2025/8okx_16933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8okx_16933/03_2025/8okx_16933.map" model { file = "/net/cci-nas-00/data/ceres_data/8okx_16933/03_2025/8okx_16933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8okx_16933/03_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-5624/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: 4.53, per 1000 atoms: 0.71 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: 1.59 Conformation dependent library (CDL) restraints added in 911.7 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: 0.83 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: 1.85 Time building geometry restraints manager: 1.89 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.550 ------------------------------------------------------------------------------- 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 : 0.758 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: 0.2359 time to fit residues: 28.8762 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 : 0.785 ------------------------------------------------------------------------------- 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 = 0.064943 restraints weight = 51459.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.065448 restraints weight = 36339.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.065519 restraints weight = 26447.706| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 MET cc_start: 0.7964 (mmm) cc_final: 0.7737 (mmt) REVERT: B 227 TRP cc_start: 0.8147 (t-100) cc_final: 0.7611 (t-100) REVERT: B 255 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7635 (mmt) outliers start: 18 outliers final: 8 residues processed: 90 average time/residue: 0.1964 time to fit residues: 23.2788 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 : 0.704 ------------------------------------------------------------------------------- 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: 0.3980 chunk 67 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 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: 8.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.087264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.060959 restraints weight = 51174.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.061164 restraints weight = 36678.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.061765 restraints weight = 28837.581| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6535 Z= 0.413 Angle : 0.830 11.305 8801 Z= 0.426 Chirality : 0.046 0.171 958 Planarity : 0.006 0.087 1127 Dihedral : 5.923 71.475 862 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.07 % Favored : 93.81 % Rotamer: Outliers : 3.94 % Allowed : 22.08 % Favored : 73.98 % 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: -1.23 (0.28), residues: 791 helix: -0.36 (0.32), residues: 236 sheet: -0.22 (0.48), residues: 126 loop : -1.25 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 193 HIS 0.019 0.003 HIS B 283 PHE 0.025 0.002 PHE D 4 TYR 0.018 0.002 TYR C 18 ARG 0.008 0.001 ARG D 68 *********************** 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 98 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 MET cc_start: 0.8211 (mmm) cc_final: 0.7952 (mmm) REVERT: B 227 TRP cc_start: 0.8161 (t-100) cc_final: 0.7878 (t-100) REVERT: C 80 LYS cc_start: 0.9697 (tppt) cc_final: 0.9332 (pttm) REVERT: C 83 TYR cc_start: 0.8732 (m-80) cc_final: 0.7940 (m-80) outliers start: 28 outliers final: 15 residues processed: 89 average time/residue: 0.2207 time to fit residues: 25.5442 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 : 0.782 ------------------------------------------------------------------------------- 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 370 PHE 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 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 31 VAL 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: 6.9990 chunk 59 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.0030 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.3796 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.087669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.062424 restraints weight = 53274.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.063438 restraints weight = 36107.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.063158 restraints weight = 26301.563| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6535 Z= 0.251 Angle : 0.739 12.689 8801 Z= 0.371 Chirality : 0.043 0.144 958 Planarity : 0.007 0.154 1127 Dihedral : 5.727 72.690 862 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.25 % Allowed : 24.89 % Favored : 72.86 % 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: -1.18 (0.29), residues: 791 helix: -0.29 (0.32), residues: 255 sheet: -0.62 (0.45), residues: 135 loop : -1.11 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 193 HIS 0.021 0.002 HIS B 283 PHE 0.013 0.002 PHE A 280 TYR 0.015 0.002 TYR C 18 ARG 0.016 0.001 ARG B 269 *********************** 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 84 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 MET cc_start: 0.8256 (mmm) cc_final: 0.7952 (mmm) REVERT: B 227 TRP cc_start: 0.8229 (t-100) cc_final: 0.7846 (t-100) REVERT: B 265 MET cc_start: 0.8815 (tpp) cc_final: 0.8055 (tpt) REVERT: C 83 TYR cc_start: 0.8934 (m-80) cc_final: 0.8447 (m-80) outliers start: 16 outliers final: 11 residues processed: 79 average time/residue: 0.1976 time to fit residues: 20.8396 Evaluate side-chains 75 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ILE 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 106 VAL Chi-restraints excluded: chain B residue 165 MET 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 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: 0.2980 chunk 8 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 69 optimal weight: 30.0000 chunk 66 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.088163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.062886 restraints weight = 51730.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.062761 restraints weight = 37908.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.062761 restraints weight = 31511.449| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6535 Z= 0.197 Angle : 0.703 13.354 8801 Z= 0.347 Chirality : 0.042 0.137 958 Planarity : 0.005 0.101 1127 Dihedral : 5.510 71.586 862 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.39 % Allowed : 23.35 % Favored : 74.26 % 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: -0.86 (0.30), residues: 791 helix: 0.15 (0.33), residues: 249 sheet: -0.51 (0.44), residues: 135 loop : -1.00 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 455 HIS 0.017 0.001 HIS B 283 PHE 0.015 0.001 PHE D 4 TYR 0.014 0.001 TYR C 18 ARG 0.007 0.000 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 87 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7757 (mmmt) REVERT: B 164 MET cc_start: 0.8255 (mmm) cc_final: 0.7928 (mmm) REVERT: B 227 TRP cc_start: 0.8417 (t-100) cc_final: 0.7942 (t-100) REVERT: B 265 MET cc_start: 0.9133 (tpp) cc_final: 0.8812 (tpt) REVERT: C 80 LYS cc_start: 0.9759 (tppt) cc_final: 0.9393 (ptpp) REVERT: C 83 TYR cc_start: 0.9044 (m-80) cc_final: 0.8316 (m-80) outliers start: 17 outliers final: 11 residues processed: 83 average time/residue: 0.2208 time to fit residues: 23.9262 Evaluate side-chains 78 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain D residue 13 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 13 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 40.0000 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.080923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.056765 restraints weight = 55156.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.056936 restraints weight = 35846.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.056936 restraints weight = 25569.624| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6535 Z= 0.187 Angle : 0.720 13.527 8801 Z= 0.353 Chirality : 0.042 0.133 958 Planarity : 0.005 0.077 1127 Dihedral : 5.398 70.115 862 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.09 % Allowed : 24.47 % Favored : 72.43 % 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: -0.70 (0.30), residues: 791 helix: 0.30 (0.33), residues: 248 sheet: -0.40 (0.45), residues: 135 loop : -0.92 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.015 0.001 HIS B 283 PHE 0.016 0.001 PHE D 4 TYR 0.017 0.001 TYR C 18 ARG 0.005 0.000 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 90 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7489 (mmmt) REVERT: B 164 MET cc_start: 0.8262 (mmm) cc_final: 0.7969 (mmm) REVERT: B 227 TRP cc_start: 0.8370 (t-100) cc_final: 0.7922 (t-100) REVERT: C 83 TYR cc_start: 0.9151 (m-80) cc_final: 0.8535 (m-80) REVERT: C 90 ILE cc_start: 0.6040 (tp) cc_final: 0.4677 (tp) REVERT: D 49 GLN cc_start: 0.7573 (mp10) cc_final: 0.7115 (pp30) outliers start: 22 outliers final: 14 residues processed: 86 average time/residue: 0.1988 time to fit residues: 22.5985 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 : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 239 LEU 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 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 144 LEU 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 84 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: 2.9990 chunk 39 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** B 287 GLN ** 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 = 0.4087 r_free = 0.4087 target = 0.087942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.063363 restraints weight = 52314.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.063298 restraints weight = 39248.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.063573 restraints weight = 26531.575| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6535 Z= 0.186 Angle : 0.738 14.358 8801 Z= 0.356 Chirality : 0.042 0.138 958 Planarity : 0.004 0.059 1127 Dihedral : 5.331 68.130 862 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.09 % Allowed : 25.18 % Favored : 71.73 % 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: -0.71 (0.30), residues: 791 helix: 0.24 (0.33), residues: 248 sheet: -0.48 (0.43), residues: 141 loop : -0.86 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.028 0.002 HIS B 283 PHE 0.016 0.001 PHE D 4 TYR 0.017 0.001 TYR C 18 ARG 0.004 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 89 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7488 (mmmt) REVERT: B 164 MET cc_start: 0.8184 (mmm) cc_final: 0.7877 (mmt) REVERT: B 227 TRP cc_start: 0.8464 (t-100) cc_final: 0.7968 (t-100) REVERT: B 265 MET cc_start: 0.8783 (tpt) cc_final: 0.8457 (tpt) REVERT: B 286 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8033 (tpp-160) REVERT: B 319 MET cc_start: 0.0347 (tpp) cc_final: -0.0230 (tpt) REVERT: C 83 TYR cc_start: 0.9185 (m-80) cc_final: 0.8579 (m-80) REVERT: C 90 ILE cc_start: 0.5511 (tp) cc_final: 0.4081 (tp) REVERT: D 49 GLN cc_start: 0.7941 (mp10) cc_final: 0.7464 (pp30) outliers start: 22 outliers final: 15 residues processed: 83 average time/residue: 0.2143 time to fit residues: 23.1068 Evaluate side-chains 80 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 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 297 ILE 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 144 LEU 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 286 ARG Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 84 THR 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: 0.2980 chunk 59 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.079163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.055478 restraints weight = 55207.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.056003 restraints weight = 35526.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.056003 restraints weight = 24011.843| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 6535 Z= 0.369 Angle : 0.834 13.184 8801 Z= 0.416 Chirality : 0.045 0.219 958 Planarity : 0.005 0.063 1127 Dihedral : 5.859 73.613 862 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.23 % Allowed : 25.32 % 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: -1.18 (0.29), residues: 791 helix: -0.15 (0.32), residues: 248 sheet: -0.65 (0.40), residues: 143 loop : -1.18 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 107 HIS 0.027 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 B 269 *********************** 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 90 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7721 (mmmt) REVERT: B 164 MET cc_start: 0.8164 (mmm) cc_final: 0.7775 (mmp) REVERT: B 227 TRP cc_start: 0.8596 (t-100) cc_final: 0.7926 (t-100) REVERT: B 265 MET cc_start: 0.8973 (tpt) cc_final: 0.8670 (tpt) REVERT: B 286 ARG cc_start: 0.8394 (tpt170) cc_final: 0.8114 (tpp-160) REVERT: B 319 MET cc_start: 0.1848 (tpp) cc_final: 0.1464 (mmm) REVERT: C 83 TYR cc_start: 0.9121 (m-80) cc_final: 0.7477 (m-10) REVERT: C 90 ILE cc_start: 0.5374 (tp) cc_final: 0.3846 (tp) outliers start: 23 outliers final: 16 residues processed: 84 average time/residue: 0.1975 time to fit residues: 22.1938 Evaluate side-chains 79 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 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 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 C residue 84 THR 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: 7.9990 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.0570 overall best weight: 1.3502 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.080747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.056454 restraints weight = 55674.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.056972 restraints weight = 33811.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.057157 restraints weight = 24371.032| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5009 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= 0.195 Angle : 0.794 15.131 8801 Z= 0.381 Chirality : 0.044 0.244 958 Planarity : 0.005 0.072 1127 Dihedral : 5.597 70.204 862 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.25 % Allowed : 26.44 % Favored : 71.31 % 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: -0.89 (0.29), residues: 791 helix: 0.23 (0.33), residues: 249 sheet: -0.64 (0.42), residues: 134 loop : -1.04 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 455 HIS 0.027 0.001 HIS B 283 PHE 0.026 0.001 PHE C 109 TYR 0.016 0.001 TYR C 18 ARG 0.007 0.001 ARG B 269 *********************** 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 82 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7562 (mmmt) REVERT: B 155 MET cc_start: 0.8780 (mmm) cc_final: 0.8549 (mmm) REVERT: B 164 MET cc_start: 0.8085 (mmm) cc_final: 0.7755 (mmt) REVERT: B 227 TRP cc_start: 0.8458 (t-100) cc_final: 0.7782 (t-100) REVERT: B 265 MET cc_start: 0.8975 (tpt) cc_final: 0.8716 (tpt) REVERT: B 268 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.9219 (p) REVERT: B 319 MET cc_start: 0.0139 (tpp) cc_final: -0.0751 (tpp) REVERT: C 83 TYR cc_start: 0.8110 (m-80) cc_final: 0.7805 (m-10) REVERT: C 90 ILE cc_start: 0.5334 (tp) cc_final: 0.3855 (tp) outliers start: 16 outliers final: 12 residues processed: 79 average time/residue: 0.2239 time to fit residues: 22.9359 Evaluate side-chains 75 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 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 165 MET Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 223 HIS 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 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: 0.8980 chunk 67 optimal weight: 30.0000 chunk 56 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.080059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.055873 restraints weight = 55602.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.056304 restraints weight = 34531.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.056643 restraints weight = 25382.529| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6535 Z= 0.284 Angle : 0.860 13.553 8801 Z= 0.418 Chirality : 0.046 0.292 958 Planarity : 0.005 0.070 1127 Dihedral : 5.711 69.997 862 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.11 % Allowed : 27.00 % Favored : 70.89 % 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: -1.13 (0.29), residues: 791 helix: -0.06 (0.33), residues: 249 sheet: -0.69 (0.42), residues: 134 loop : -1.16 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 227 HIS 0.025 0.002 HIS B 283 PHE 0.025 0.002 PHE C 109 TYR 0.016 0.002 TYR C 18 ARG 0.017 0.001 ARG C 82 ********************** 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 78 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7552 (mmmt) REVERT: B 164 MET cc_start: 0.8060 (mmm) cc_final: 0.7618 (mmt) REVERT: B 227 TRP cc_start: 0.8562 (t-100) cc_final: 0.7920 (t-100) REVERT: B 265 MET cc_start: 0.9051 (tpt) cc_final: 0.8777 (tpt) REVERT: B 268 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9188 (p) REVERT: B 286 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.8016 (tpp-160) REVERT: C 90 ILE cc_start: 0.5766 (tp) cc_final: 0.4357 (tp) REVERT: D 49 GLN cc_start: 0.7119 (mp10) cc_final: 0.6914 (pm20) outliers start: 15 outliers final: 13 residues processed: 75 average time/residue: 0.2136 time to fit residues: 20.9875 Evaluate side-chains 76 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 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 165 MET 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 268 THR Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU 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: 7.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4054 r_free = 0.4054 target = 0.086780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.061736 restraints weight = 54161.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.061737 restraints weight = 35696.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.061737 restraints weight = 35685.282| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6535 Z= 0.269 Angle : 0.858 13.617 8801 Z= 0.414 Chirality : 0.047 0.311 958 Planarity : 0.005 0.069 1127 Dihedral : 5.699 68.655 862 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % 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: -1.18 (0.29), residues: 791 helix: -0.03 (0.33), residues: 249 sheet: -0.79 (0.41), residues: 134 loop : -1.22 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 227 HIS 0.025 0.002 HIS B 283 PHE 0.027 0.002 PHE C 109 TYR 0.017 0.001 TYR C 18 ARG 0.030 0.001 ARG C 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3324.97 seconds wall clock time: 57 minutes 56.78 seconds (3476.78 seconds total)