Starting phenix.real_space_refine on Sat Aug 23 00:40:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8okx_16933/08_2025/8okx_16933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8okx_16933/08_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_16933/08_2025/8okx_16933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8okx_16933/08_2025/8okx_16933.map" model { file = "/net/cci-nas-00/data/ceres_data/8okx_16933/08_2025/8okx_16933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8okx_16933/08_2025/8okx_16933.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.95, per 1000 atoms: 0.30 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: 0.71 Conformation dependent library (CDL) restraints added in 440.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.07 Time building geometry restraints manager: 0.90 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.760 Find NCS groups from input model: 0.030 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- 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 6539 Z= 0.393 Angle : 0.989 21.749 8804 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG B 269 TYR 0.085 0.004 TYR A 510 PHE 0.044 0.002 PHE B 127 TRP 0.022 0.002 TRP B 107 HIS 0.010 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00970 ( 6535) covalent geometry : angle 0.98791 ( 8801) hydrogen bonds : bond 0.22468 ( 262) hydrogen bonds : angle 8.52240 ( 732) metal coordination : bond 0.00554 ( 4) metal coordination : angle 2.98119 ( 3) *********************** 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 : 0.279 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: -0.2327 (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: 0.1129 time to fit residues: 13.8998 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 : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0010 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 50.0000 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.090237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.065242 restraints weight = 51951.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.065072 restraints weight = 36389.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.065296 restraints weight = 26598.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.065307 restraints weight = 22762.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.065307 restraints weight = 22643.334| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6539 Z= 0.164 Angle : 0.741 12.088 8804 Z= 0.372 Chirality : 0.044 0.188 958 Planarity : 0.007 0.139 1127 Dihedral : 5.274 62.321 862 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.31 % Favored : 94.56 % Rotamer: Outliers : 2.53 % Allowed : 20.53 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.30), residues: 791 helix: 0.35 (0.34), residues: 241 sheet: -0.35 (0.47), residues: 131 loop : -1.02 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 33 TYR 0.016 0.001 TYR C 18 PHE 0.019 0.002 PHE B 210 TRP 0.011 0.002 TRP B 193 HIS 0.020 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6535) covalent geometry : angle 0.73920 ( 8801) hydrogen bonds : bond 0.04920 ( 262) hydrogen bonds : angle 6.12794 ( 732) metal coordination : bond 0.00674 ( 4) metal coordination : angle 2.74004 ( 3) *********************** 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 : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7807 (mmmt) REVERT: B 227 TRP cc_start: 0.8121 (t-100) cc_final: 0.7585 (t-100) REVERT: B 255 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7734 (mmt) outliers start: 18 outliers final: 8 residues processed: 90 average time/residue: 0.0953 time to fit residues: 11.3339 Evaluate side-chains 79 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 LYS 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 68 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.087203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.061131 restraints weight = 50732.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.061131 restraints weight = 37003.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.061131 restraints weight = 37003.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.061131 restraints weight = 37003.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.061131 restraints weight = 37003.452| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6539 Z= 0.269 Angle : 0.798 10.870 8804 Z= 0.409 Chirality : 0.045 0.173 958 Planarity : 0.006 0.073 1127 Dihedral : 5.867 70.622 862 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.32 % Favored : 93.55 % Rotamer: Outliers : 3.94 % Allowed : 21.38 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.29), residues: 791 helix: -0.24 (0.32), residues: 236 sheet: -0.17 (0.48), residues: 128 loop : -1.13 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 68 TYR 0.019 0.002 TYR C 18 PHE 0.027 0.002 PHE D 4 TRP 0.013 0.002 TRP B 193 HIS 0.017 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00569 ( 6535) covalent geometry : angle 0.79674 ( 8801) hydrogen bonds : bond 0.04839 ( 262) hydrogen bonds : angle 6.03588 ( 732) metal coordination : bond 0.01164 ( 4) metal coordination : angle 2.68685 ( 3) *********************** 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 : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 MET cc_start: 0.8030 (mmt) cc_final: 0.7795 (mmm) REVERT: B 227 TRP cc_start: 0.8201 (t-100) cc_final: 0.7875 (t-100) REVERT: C 80 LYS cc_start: 0.9724 (tppt) cc_final: 0.9307 (pttp) REVERT: C 83 TYR cc_start: 0.8844 (m-80) cc_final: 0.8151 (m-80) REVERT: D 6 MET cc_start: 0.6293 (tpp) cc_final: 0.6090 (tpp) outliers start: 28 outliers final: 15 residues processed: 89 average time/residue: 0.0987 time to fit residues: 11.4112 Evaluate side-chains 84 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 252 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 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 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 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 74 optimal weight: 0.0970 chunk 38 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.088170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.062755 restraints weight = 52163.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.062755 restraints weight = 35423.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.062755 restraints weight = 35423.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.062755 restraints weight = 35423.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.062755 restraints weight = 35423.634| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6539 Z= 0.144 Angle : 0.719 12.622 8804 Z= 0.356 Chirality : 0.043 0.135 958 Planarity : 0.006 0.143 1127 Dihedral : 5.553 69.778 862 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.67 % Allowed : 23.91 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.30), residues: 791 helix: -0.07 (0.32), residues: 249 sheet: -0.58 (0.45), residues: 136 loop : -0.82 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 269 TYR 0.014 0.001 TYR C 18 PHE 0.011 0.001 PHE A 280 TRP 0.007 0.001 TRP B 193 HIS 0.017 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6535) covalent geometry : angle 0.71768 ( 8801) hydrogen bonds : bond 0.03985 ( 262) hydrogen bonds : angle 5.59151 ( 732) metal coordination : bond 0.00595 ( 4) metal coordination : angle 2.62453 ( 3) *********************** 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 90 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 GLU cc_start: 0.8845 (tp30) cc_final: 0.8354 (tm-30) REVERT: B 227 TRP cc_start: 0.8285 (t-100) cc_final: 0.7827 (t-100) REVERT: B 265 MET cc_start: 0.9410 (mtm) cc_final: 0.9135 (mmm) REVERT: C 83 TYR cc_start: 0.9003 (m-80) cc_final: 0.8551 (m-80) REVERT: D 6 MET cc_start: 0.5999 (tpp) cc_final: 0.5722 (tpp) outliers start: 19 outliers final: 12 residues processed: 84 average time/residue: 0.0950 time to fit residues: 10.5261 Evaluate side-chains 77 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 252 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 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 62 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** B 287 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.087783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.062488 restraints weight = 53190.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.063531 restraints weight = 36332.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.063392 restraints weight = 24143.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.063405 restraints weight = 20880.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.063405 restraints weight = 20630.993| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 6539 Z= 0.146 Angle : 0.706 12.854 8804 Z= 0.350 Chirality : 0.042 0.137 958 Planarity : 0.005 0.072 1127 Dihedral : 5.471 69.532 862 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.81 % Allowed : 23.35 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.30), residues: 791 helix: 0.12 (0.33), residues: 248 sheet: -0.52 (0.45), residues: 135 loop : -0.85 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 68 TYR 0.028 0.002 TYR B 102 PHE 0.015 0.001 PHE D 4 TRP 0.007 0.001 TRP B 193 HIS 0.015 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6535) covalent geometry : angle 0.70415 ( 8801) hydrogen bonds : bond 0.03729 ( 262) hydrogen bonds : angle 5.54841 ( 732) metal coordination : bond 0.00584 ( 4) metal coordination : angle 2.47331 ( 3) *********************** 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 90 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7404 (mmmt) REVERT: B 227 TRP cc_start: 0.8377 (t-100) cc_final: 0.7874 (t-100) REVERT: B 265 MET cc_start: 0.9288 (mtm) cc_final: 0.8983 (mmm) REVERT: C 80 LYS cc_start: 0.9748 (tppt) cc_final: 0.9397 (ptpp) REVERT: C 83 TYR cc_start: 0.9078 (m-80) cc_final: 0.8300 (m-80) REVERT: C 90 ILE cc_start: 0.5330 (tp) cc_final: 0.4007 (tp) REVERT: D 1 MET cc_start: 0.9352 (tpt) cc_final: 0.8915 (tmm) outliers start: 20 outliers final: 12 residues processed: 86 average time/residue: 0.1061 time to fit residues: 11.7075 Evaluate side-chains 80 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 252 LYS 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 144 LEU 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 D residue 13 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 68 optimal weight: 8.9990 chunk 29 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN B 236 ASN ** 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 = 0.4101 r_free = 0.4101 target = 0.088375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.063257 restraints weight = 53242.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.063260 restraints weight = 38135.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.063260 restraints weight = 38099.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.063260 restraints weight = 38099.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.063260 restraints weight = 38099.430| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6539 Z= 0.117 Angle : 0.728 13.877 8804 Z= 0.350 Chirality : 0.042 0.137 958 Planarity : 0.005 0.073 1127 Dihedral : 5.166 65.445 862 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.67 % Allowed : 22.93 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.30), residues: 791 helix: 0.28 (0.33), residues: 242 sheet: -0.40 (0.44), residues: 133 loop : -0.68 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 68 TYR 0.023 0.001 TYR B 102 PHE 0.011 0.001 PHE D 4 TRP 0.006 0.001 TRP B 193 HIS 0.011 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6535) covalent geometry : angle 0.72651 ( 8801) hydrogen bonds : bond 0.03399 ( 262) hydrogen bonds : angle 5.34286 ( 732) metal coordination : bond 0.00437 ( 4) metal coordination : angle 2.30870 ( 3) *********************** 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: 19 poor density : 71 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7791 (mmmt) REVERT: B 227 TRP cc_start: 0.8451 (t-100) cc_final: 0.7961 (t-100) REVERT: B 265 MET cc_start: 0.9426 (mtm) cc_final: 0.9016 (mmm) REVERT: C 83 TYR cc_start: 0.9057 (m-80) cc_final: 0.7599 (m-10) REVERT: C 90 ILE cc_start: 0.4528 (tp) cc_final: 0.3266 (tp) REVERT: D 1 MET cc_start: 0.9330 (tpt) cc_final: 0.8863 (tmm) REVERT: D 6 MET cc_start: 0.6271 (tpp) cc_final: 0.6046 (tpp) REVERT: D 49 GLN cc_start: 0.7783 (mp10) cc_final: 0.7364 (pp30) outliers start: 19 outliers final: 9 residues processed: 87 average time/residue: 0.0928 time to fit residues: 10.7381 Evaluate side-chains 74 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 270 SER Chi-restraints excluded: chain B residue 299 LEU 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 20 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.0170 chunk 24 optimal weight: 0.6980 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** 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 = 0.4096 r_free = 0.4096 target = 0.088292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.063350 restraints weight = 52435.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.063417 restraints weight = 38136.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.063909 restraints weight = 30043.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.063828 restraints weight = 22723.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.063893 restraints weight = 21418.354| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6539 Z= 0.125 Angle : 0.751 14.452 8804 Z= 0.358 Chirality : 0.042 0.135 958 Planarity : 0.005 0.065 1127 Dihedral : 5.184 63.210 862 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.97 % Allowed : 25.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.30), residues: 791 helix: 0.26 (0.33), residues: 249 sheet: -0.38 (0.43), residues: 136 loop : -0.77 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 269 TYR 0.017 0.001 TYR C 18 PHE 0.015 0.001 PHE C 109 TRP 0.007 0.001 TRP B 193 HIS 0.021 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6535) covalent geometry : angle 0.74969 ( 8801) hydrogen bonds : bond 0.03413 ( 262) hydrogen bonds : angle 5.39821 ( 732) metal coordination : bond 0.00491 ( 4) metal coordination : angle 2.49497 ( 3) *********************** 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 80 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7498 (mmmt) REVERT: B 227 TRP cc_start: 0.8451 (t-100) cc_final: 0.7969 (t-100) REVERT: B 265 MET cc_start: 0.9276 (mtm) cc_final: 0.8900 (mmm) REVERT: C 83 TYR cc_start: 0.8142 (m-80) cc_final: 0.7789 (m-10) REVERT: C 90 ILE cc_start: 0.5203 (tp) cc_final: 0.3768 (tp) REVERT: D 6 MET cc_start: 0.5949 (tpp) cc_final: 0.5730 (tpp) REVERT: D 49 GLN cc_start: 0.7858 (mp10) cc_final: 0.7409 (pp30) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.1055 time to fit residues: 10.5182 Evaluate side-chains 74 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 30.0000 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN ** 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 = 0.4100 r_free = 0.4100 target = 0.088453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.063722 restraints weight = 51807.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.063525 restraints weight = 39606.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.064040 restraints weight = 30589.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.063820 restraints weight = 22931.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.063820 restraints weight = 19471.348| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6539 Z= 0.119 Angle : 0.770 15.337 8804 Z= 0.366 Chirality : 0.043 0.238 958 Planarity : 0.005 0.065 1127 Dihedral : 5.070 59.940 862 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.39 % Allowed : 24.47 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.30), residues: 791 helix: 0.39 (0.34), residues: 243 sheet: -0.20 (0.45), residues: 130 loop : -0.63 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 82 TYR 0.014 0.001 TYR C 18 PHE 0.017 0.001 PHE C 109 TRP 0.006 0.001 TRP B 193 HIS 0.022 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6535) covalent geometry : angle 0.76848 ( 8801) hydrogen bonds : bond 0.03346 ( 262) hydrogen bonds : angle 5.33862 ( 732) metal coordination : bond 0.00488 ( 4) metal coordination : angle 2.55777 ( 3) *********************** 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 84 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7558 (mmmt) REVERT: B 227 TRP cc_start: 0.8509 (t-100) cc_final: 0.7922 (t-100) REVERT: B 319 MET cc_start: 0.0993 (ttt) cc_final: 0.0290 (tpp) REVERT: C 83 TYR cc_start: 0.8265 (m-80) cc_final: 0.7275 (m-10) REVERT: C 90 ILE cc_start: 0.5669 (tp) cc_final: 0.4208 (tp) REVERT: D 6 MET cc_start: 0.5955 (tpp) cc_final: 0.5708 (tpp) REVERT: D 49 GLN cc_start: 0.7938 (mp10) cc_final: 0.7470 (pp30) outliers start: 17 outliers final: 11 residues processed: 82 average time/residue: 0.0990 time to fit residues: 10.5326 Evaluate side-chains 76 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 144 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** 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 = 0.4058 r_free = 0.4058 target = 0.086851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.061563 restraints weight = 53254.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.061610 restraints weight = 36970.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.061610 restraints weight = 29700.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.061610 restraints weight = 29697.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.061610 restraints weight = 29697.923| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6539 Z= 0.210 Angle : 0.850 12.601 8804 Z= 0.414 Chirality : 0.045 0.223 958 Planarity : 0.006 0.096 1127 Dihedral : 5.422 62.550 862 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.39 % Allowed : 25.32 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.30), residues: 791 helix: 0.00 (0.33), residues: 249 sheet: -0.63 (0.42), residues: 136 loop : -0.80 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 82 TYR 0.020 0.002 TYR C 83 PHE 0.020 0.002 PHE C 109 TRP 0.009 0.002 TRP B 193 HIS 0.022 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 6535) covalent geometry : angle 0.84876 ( 8801) hydrogen bonds : bond 0.04096 ( 262) hydrogen bonds : angle 5.92215 ( 732) metal coordination : bond 0.00706 ( 4) metal coordination : angle 2.79360 ( 3) *********************** 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 81 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7954 (mmmt) REVERT: B 227 TRP cc_start: 0.8568 (t-100) cc_final: 0.7950 (t-100) REVERT: B 319 MET cc_start: 0.3675 (ttt) cc_final: 0.2849 (tpp) REVERT: C 82 ARG cc_start: 0.5307 (pmt170) cc_final: 0.4949 (pmt170) REVERT: C 83 TYR cc_start: 0.8495 (m-80) cc_final: 0.8117 (m-10) REVERT: C 90 ILE cc_start: 0.4674 (tp) cc_final: 0.3254 (tp) REVERT: D 1 MET cc_start: 0.9264 (tpt) cc_final: 0.8890 (tmm) REVERT: D 6 MET cc_start: 0.6403 (tpp) cc_final: 0.6165 (tpp) REVERT: D 49 GLN cc_start: 0.7513 (mp10) cc_final: 0.6979 (pp30) outliers start: 17 outliers final: 13 residues processed: 77 average time/residue: 0.0957 time to fit residues: 9.8215 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 : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 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 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 88 THR 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 11 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 77 optimal weight: 0.0670 chunk 50 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4097 r_free = 0.4097 target = 0.088225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.062599 restraints weight = 52394.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.062614 restraints weight = 35759.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.062614 restraints weight = 34569.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.062614 restraints weight = 34569.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.062614 restraints weight = 34568.862| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 6539 Z= 0.127 Angle : 0.861 16.392 8804 Z= 0.402 Chirality : 0.046 0.293 958 Planarity : 0.005 0.060 1127 Dihedral : 5.202 56.775 862 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.97 % Allowed : 25.88 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.30), residues: 791 helix: 0.23 (0.34), residues: 239 sheet: -0.41 (0.43), residues: 130 loop : -0.71 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 82 TYR 0.015 0.001 TYR B 102 PHE 0.031 0.001 PHE C 109 TRP 0.006 0.001 TRP A 455 HIS 0.021 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6535) covalent geometry : angle 0.86010 ( 8801) hydrogen bonds : bond 0.03576 ( 262) hydrogen bonds : angle 5.68485 ( 732) metal coordination : bond 0.00703 ( 4) metal coordination : angle 2.56299 ( 3) ********************** 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: 14 poor density : 64 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7828 (mmmt) REVERT: B 227 TRP cc_start: 0.8477 (t-100) cc_final: 0.7843 (t-100) REVERT: B 286 ARG cc_start: 0.7851 (tpm170) cc_final: 0.7237 (tpm170) REVERT: B 319 MET cc_start: 0.3825 (ttt) cc_final: 0.2280 (tpp) REVERT: C 83 TYR cc_start: 0.8288 (m-80) cc_final: 0.7706 (m-10) REVERT: C 90 ILE cc_start: 0.4217 (tp) cc_final: 0.2884 (tp) REVERT: D 1 MET cc_start: 0.9229 (tpt) cc_final: 0.8890 (ppp) REVERT: D 6 MET cc_start: 0.6324 (tpp) cc_final: 0.5801 (tpp) REVERT: D 49 GLN cc_start: 0.7691 (mp10) cc_final: 0.7250 (pp30) outliers start: 14 outliers final: 12 residues processed: 76 average time/residue: 0.0955 time to fit residues: 9.6801 Evaluate side-chains 75 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4089 r_free = 0.4089 target = 0.080011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.055685 restraints weight = 55770.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.056316 restraints weight = 35161.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.056428 restraints weight = 23306.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.056631 restraints weight = 19239.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.056802 restraints weight = 17426.998| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 6539 Z= 0.211 Angle : 0.885 12.593 8804 Z= 0.426 Chirality : 0.046 0.289 958 Planarity : 0.006 0.099 1127 Dihedral : 5.380 58.281 862 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.97 % Allowed : 25.46 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.29), residues: 791 helix: 0.01 (0.33), residues: 242 sheet: -0.65 (0.41), residues: 136 loop : -0.95 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 82 TYR 0.017 0.002 TYR C 18 PHE 0.032 0.002 PHE D 4 TRP 0.010 0.001 TRP B 227 HIS 0.020 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 6535) covalent geometry : angle 0.88297 ( 8801) hydrogen bonds : bond 0.04097 ( 262) hydrogen bonds : angle 6.00325 ( 732) metal coordination : bond 0.00725 ( 4) metal coordination : angle 2.99874 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2153.90 seconds wall clock time: 37 minutes 46.50 seconds (2266.50 seconds total)