Starting phenix.real_space_refine on Fri Jul 3 11:23:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jzv_22581/07_2026/7jzv_22581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzv_22581/07_2026/7jzv_22581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jzv_22581/07_2026/7jzv_22581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzv_22581/07_2026/7jzv_22581.map" model { file = "/net/cci-nas-00/data/ceres_data/7jzv_22581/07_2026/7jzv_22581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzv_22581/07_2026/7jzv_22581.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jzv_22581/07_2026/7jzv_22581.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jzv_22581/07_2026/7jzv_22581.cif" } resolution = 3.9 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= -0.000 sd= 0.341 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 278 5.49 5 S 40 5.16 5 C 8141 2.51 5 N 2655 2.21 5 O 3221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14339 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1995 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 233} Chain: "B" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 753 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "N" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 801 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "O" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "P" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 737 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "Q" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "X" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2867 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "Y" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2832 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "n" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 801 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "o" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "p" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 738 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "q" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 158 SG CYS A 24 39.145 94.485 61.272 1.00 0.00 S ATOM 179 SG CYS A 27 39.227 98.258 60.501 1.00 0.00 S ATOM 315 SG CYS A 44 40.524 95.739 57.903 1.00 0.00 S ATOM 341 SG CYS A 47 42.509 96.352 61.146 1.00 0.00 S ATOM 272 SG CYS A 39 39.960 81.280 58.237 1.00 0.00 S ATOM 449 SG CYS A 61 40.030 83.271 61.518 1.00 0.00 S ATOM 470 SG CYS A 64 38.101 79.951 61.319 1.00 0.00 S ATOM 2193 SG CYS B 50 32.099 79.651 33.041 1.00 0.00 S ATOM 2216 SG CYS B 53 31.426 80.808 36.612 1.00 0.00 S ATOM 2353 SG CYS B 71 29.123 78.212 35.069 1.00 0.00 S ATOM 2373 SG CYS B 74 32.738 77.193 35.933 1.00 0.00 S ATOM 2309 SG CYS B 66 43.282 80.267 39.532 1.00 0.00 S ATOM 2429 SG CYS B 83 41.408 78.130 36.901 1.00 0.00 S ATOM 2449 SG CYS B 86 44.672 79.930 35.954 1.00 0.00 S Time building chain proxies: 2.87, per 1000 atoms: 0.20 Number of scatterers: 14339 At special positions: 0 Unit cell: (121.8, 124.95, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 40 16.00 P 278 15.00 O 3221 8.00 N 2655 7.00 C 8141 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: 0.89 Conformation dependent library (CDL) restraints added in 319.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 44 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 27 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 47 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 24 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" NE2 HIS A 41 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 64 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 61 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 39 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 53 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 50 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 74 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" ND1 HIS B 68 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 86 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 66 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 83 " Number of angles added : 18 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 64.9% alpha, 4.8% beta 137 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 7 through 22 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 77 through 97 removed outlier: 3.930A pdb=" N LEU A 95 " --> pdb=" O CYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.528A pdb=" N CYS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 4.993A pdb=" N ILE A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 removed outlier: 4.045A pdb=" N LYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 46 removed outlier: 3.746A pdb=" N GLY B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 81 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 98 through 122 Processing helix chain 'N' and resid 16 through 21 Processing helix chain 'N' and resid 26 through 37 Processing helix chain 'N' and resid 46 through 73 Processing helix chain 'N' and resid 79 through 90 Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'N' and resid 112 through 116 Processing helix chain 'O' and resid 37 through 47 Processing helix chain 'O' and resid 55 through 84 Processing helix chain 'O' and resid 90 through 102 Processing helix chain 'O' and resid 105 through 124 Processing helix chain 'P' and resid 47 through 57 Processing helix chain 'P' and resid 63 through 76 Processing helix chain 'P' and resid 85 through 114 Processing helix chain 'P' and resid 120 through 132 Processing helix chain 'Q' and resid 24 through 29 Processing helix chain 'Q' and resid 30 through 41 Processing helix chain 'Q' and resid 49 through 76 Processing helix chain 'Q' and resid 82 through 93 Processing helix chain 'n' and resid 16 through 22 Processing helix chain 'n' and resid 26 through 37 Processing helix chain 'n' and resid 46 through 73 Processing helix chain 'n' and resid 79 through 89 Processing helix chain 'n' and resid 90 through 98 Processing helix chain 'n' and resid 112 through 116 Processing helix chain 'o' and resid 37 through 49 Processing helix chain 'o' and resid 55 through 84 Processing helix chain 'o' and resid 90 through 102 Processing helix chain 'o' and resid 103 through 124 removed outlier: 3.585A pdb=" N LYS o 108 " --> pdb=" O GLY o 104 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 56 Processing helix chain 'p' and resid 63 through 76 Processing helix chain 'p' and resid 85 through 114 Processing helix chain 'p' and resid 120 through 133 Processing helix chain 'q' and resid 25 through 29 Processing helix chain 'q' and resid 30 through 41 Processing helix chain 'q' and resid 49 through 76 removed outlier: 3.707A pdb=" N GLU q 53 " --> pdb=" O LEU q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 82 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 4.279A pdb=" N SER A 59 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 225 Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 70 removed outlier: 5.266A pdb=" N HIS B 68 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU B 63 " --> pdb=" O HIS B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 42 through 43 removed outlier: 7.042A pdb=" N ARG N 42 " --> pdb=" O ILE O 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'N' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'N' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'P' and resid 83 through 84 removed outlier: 7.096A pdb=" N ARG P 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'P' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'Q' and resid 96 through 98 removed outlier: 6.713A pdb=" N THR Q 96 " --> pdb=" O THR n 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'n' and resid 42 through 43 removed outlier: 6.992A pdb=" N ARG n 42 " --> pdb=" O ILE o 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'n' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'p' and resid 83 through 84 removed outlier: 6.743A pdb=" N ARG p 83 " --> pdb=" O VAL q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'p' and resid 118 through 119 541 hydrogen bonds defined for protein. 1578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 702 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3799 1.34 - 1.49: 5485 1.49 - 1.63: 5793 1.63 - 1.77: 28 1.77 - 1.92: 53 Bond restraints: 15158 Sorted by residual: bond pdb=" NE ARG p 134 " pdb=" CZ ARG p 134 " ideal model delta sigma weight residual 1.326 1.376 -0.050 1.10e-02 8.26e+03 2.06e+01 bond pdb=" CB HIS p 113 " pdb=" CG HIS p 113 " ideal model delta sigma weight residual 1.497 1.434 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" CA CYS B 53 " pdb=" CB CYS B 53 " ideal model delta sigma weight residual 1.524 1.593 -0.068 1.53e-02 4.27e+03 1.99e+01 bond pdb=" CB HIS P 113 " pdb=" CG HIS P 113 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" CB HIS Q 75 " pdb=" CG HIS Q 75 " ideal model delta sigma weight residual 1.497 1.438 0.059 1.40e-02 5.10e+03 1.76e+01 ... (remaining 15153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 20084 2.42 - 4.84: 1369 4.84 - 7.26: 191 7.26 - 9.68: 18 9.68 - 12.10: 1 Bond angle restraints: 21663 Sorted by residual: angle pdb=" C LYS A 263 " pdb=" N PRO A 264 " pdb=" CA PRO A 264 " ideal model delta sigma weight residual 119.66 126.00 -6.34 7.30e-01 1.88e+00 7.54e+01 angle pdb=" C HIS O 49 " pdb=" N PRO O 50 " pdb=" CA PRO O 50 " ideal model delta sigma weight residual 119.56 128.20 -8.64 1.01e+00 9.80e-01 7.32e+01 angle pdb=" C PRO A 264 " pdb=" N PRO A 265 " pdb=" CA PRO A 265 " ideal model delta sigma weight residual 120.31 128.06 -7.75 9.80e-01 1.04e+00 6.25e+01 angle pdb=" C ASP A 312 " pdb=" N PRO A 313 " pdb=" CA PRO A 313 " ideal model delta sigma weight residual 119.92 128.19 -8.27 1.07e+00 8.73e-01 5.97e+01 angle pdb=" C GLY A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.92 127.81 -7.89 1.07e+00 8.73e-01 5.44e+01 ... (remaining 21658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.39: 6719 25.39 - 50.77: 1311 50.77 - 76.16: 422 76.16 - 101.54: 7 101.54 - 126.93: 1 Dihedral angle restraints: 8460 sinusoidal: 5291 harmonic: 3169 Sorted by residual: dihedral pdb=" CA HIS O 49 " pdb=" C HIS O 49 " pdb=" N PRO O 50 " pdb=" CA PRO O 50 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" C4' DT Y 53 " pdb=" C3' DT Y 53 " pdb=" O3' DT Y 53 " pdb=" P DT Y 54 " ideal model delta sinusoidal sigma weight residual 220.00 93.07 126.93 1 3.50e+01 8.16e-04 1.25e+01 dihedral pdb=" CA PRO o 103 " pdb=" C PRO o 103 " pdb=" N GLY o 104 " pdb=" CA GLY o 104 " ideal model delta harmonic sigma weight residual 180.00 163.90 16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 8457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1765 0.071 - 0.142: 589 0.142 - 0.212: 98 0.212 - 0.283: 5 0.283 - 0.354: 2 Chirality restraints: 2459 Sorted by residual: chirality pdb=" CA CYS B 71 " pdb=" N CYS B 71 " pdb=" C CYS B 71 " pdb=" CB CYS B 71 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA CYS B 53 " pdb=" N CYS B 53 " pdb=" C CYS B 53 " pdb=" CB CYS B 53 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ARG N 88 " pdb=" N ARG N 88 " pdb=" C ARG N 88 " pdb=" CB ARG N 88 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2456 not shown) Planarity restraints: 1791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 347 " 0.024 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C MET A 347 " -0.084 2.00e-02 2.50e+03 pdb=" O MET A 347 " 0.030 2.00e-02 2.50e+03 pdb=" OXT MET A 347 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 102 " -0.024 2.00e-02 2.50e+03 4.85e-02 2.36e+01 pdb=" C GLY Q 102 " 0.084 2.00e-02 2.50e+03 pdb=" O GLY Q 102 " -0.030 2.00e-02 2.50e+03 pdb=" OXT GLY Q 102 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 293 " -0.037 2.00e-02 2.50e+03 1.79e-02 8.05e+00 pdb=" CG TRP A 293 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 293 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 293 " 0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP A 293 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 293 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 293 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 293 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 293 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 293 " -0.020 2.00e-02 2.50e+03 ... (remaining 1788 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 422 2.67 - 3.23: 12480 3.23 - 3.79: 24765 3.79 - 4.34: 34308 4.34 - 4.90: 47805 Nonbonded interactions: 119780 Sorted by model distance: nonbonded pdb=" OG1 THR Q 30 " pdb=" OP2 DA X 58 " model vdw 2.117 3.040 nonbonded pdb=" OP1 DC X 77 " pdb=" OG SER q 47 " model vdw 2.261 3.040 nonbonded pdb=" O ARG A 71 " pdb=" OG SER A 72 " model vdw 2.300 3.040 nonbonded pdb=" OP1 DG Y 67 " pdb=" N VAL p 117 " model vdw 2.306 3.120 nonbonded pdb=" OG SER O 32 " pdb=" OP1 DC X 100 " model vdw 2.334 3.040 ... (remaining 119775 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 Found NCS groups: ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = (chain 'o' and resid 31 through 124) } ncs_group { reference = (chain 'P' and resid 46 through 134) selection = (chain 'p' and resid 46 through 134) } ncs_group { reference = (chain 'Q' and resid 25 through 102) selection = chain 'q' } 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: 1.360 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.510 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 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 : 0.013 0.109 15174 Z= 0.800 Angle : 1.353 12.099 21681 Z= 1.092 Chirality : 0.068 0.354 2459 Planarity : 0.004 0.049 1791 Dihedral : 24.149 126.927 6410 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.49 % Favored : 98.32 % Rotamer: Outliers : 0.22 % Allowed : 0.32 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.23), residues: 1073 helix: 0.62 (0.17), residues: 676 sheet: -0.17 (1.32), residues: 18 loop : 0.29 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG n 20 TYR 0.026 0.003 TYR o 40 PHE 0.015 0.003 PHE p 67 TRP 0.037 0.006 TRP A 293 HIS 0.004 0.001 HIS O 109 Details of bonding type rmsd/Z covalent geometry : bond 0.01251 / 0.80 (15158) covalent geometry : angle 1.35288 / 1.09 (21663) hydrogen bonds : bond 0.19128 / 12.47 ( 892) hydrogen bonds : angle 5.82510 / 4.15 ( 2280) metal coordination : bond 0.03260 / 2.17 ( 16) metal coordination : angle 1.84034 / 1.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 327 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.5569 (tt0) cc_final: 0.5320 (tt0) REVERT: A 25 PRO cc_start: 0.7787 (Cg_exo) cc_final: 0.7279 (Cg_endo) REVERT: A 52 LEU cc_start: 0.7041 (mt) cc_final: 0.5730 (mt) REVERT: N 39 TYR cc_start: 0.8373 (m-80) cc_final: 0.8000 (m-80) REVERT: O 36 SER cc_start: 0.8125 (p) cc_final: 0.7808 (m) REVERT: O 108 LYS cc_start: 0.7870 (mttt) cc_final: 0.7265 (mtpt) REVERT: P 60 LEU cc_start: 0.7035 (mt) cc_final: 0.6811 (mt) REVERT: Q 52 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6911 (mm-30) REVERT: Q 53 GLU cc_start: 0.7836 (tp30) cc_final: 0.7453 (tp30) REVERT: p 60 LEU cc_start: 0.8272 (mt) cc_final: 0.7723 (mt) outliers start: 2 outliers final: 0 residues processed: 329 average time/residue: 0.1241 time to fit residues: 56.5083 Evaluate side-chains 251 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN O 84 ASN P 113 HIS P 125 GLN Q 25 ASN ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 55 GLN p 76 GLN q 25 ASN q 93 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.221939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.150372 restraints weight = 21982.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.155557 restraints weight = 11216.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.158792 restraints weight = 7646.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.160451 restraints weight = 6257.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.161576 restraints weight = 5667.689| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 15174 Z= 0.192 Angle : 0.988 43.675 21681 Z= 0.462 Chirality : 0.051 0.282 2459 Planarity : 0.005 0.045 1791 Dihedral : 28.026 146.802 4242 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.58 % Favored : 98.32 % Rotamer: Outliers : 2.80 % Allowed : 8.92 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.24), residues: 1073 helix: 1.76 (0.19), residues: 676 sheet: 0.21 (1.22), residues: 18 loop : -0.19 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG q 78 TYR 0.029 0.002 TYR B 87 PHE 0.020 0.003 PHE P 67 TRP 0.014 0.002 TRP A 293 HIS 0.013 0.002 HIS B 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 (15158) covalent geometry : angle 0.78247 / 0.45 (21663) hydrogen bonds : bond 0.09755 / 6.39 ( 892) hydrogen bonds : angle 4.13428 / 2.96 ( 2280) metal coordination : bond 0.01913 / 1.05 ( 16) metal coordination : angle 20.95883 / 14.96 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 290 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8946 (tpp) cc_final: 0.8713 (tpp) REVERT: A 52 LEU cc_start: 0.8720 (mt) cc_final: 0.8232 (mt) REVERT: A 71 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7963 (mtm110) REVERT: A 204 LYS cc_start: 0.8109 (tppt) cc_final: 0.7846 (tppp) REVERT: B 104 MET cc_start: 0.8159 (mmm) cc_final: 0.7790 (mmm) REVERT: N 23 LEU cc_start: 0.8974 (mt) cc_final: 0.8661 (mt) REVERT: N 77 ARG cc_start: 0.7548 (ptp-170) cc_final: 0.7188 (ptp-170) REVERT: N 95 LYS cc_start: 0.8893 (tppt) cc_final: 0.7853 (tptt) REVERT: O 36 SER cc_start: 0.8530 (p) cc_final: 0.8262 (m) REVERT: O 108 LYS cc_start: 0.8837 (mttt) cc_final: 0.8204 (mtpt) REVERT: O 116 LYS cc_start: 0.8536 (ttpp) cc_final: 0.8000 (tttp) REVERT: P 93 GLN cc_start: 0.8799 (tt0) cc_final: 0.8584 (tt0) REVERT: Q 35 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.7548 (mtp85) REVERT: Q 52 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7767 (mm-30) REVERT: Q 74 GLU cc_start: 0.8179 (tt0) cc_final: 0.7852 (tt0) REVERT: n 84 GLN cc_start: 0.8089 (tt0) cc_final: 0.7799 (tt0) REVERT: n 88 ARG cc_start: 0.7552 (mmt180) cc_final: 0.7228 (tpp80) REVERT: p 125 GLN cc_start: 0.8271 (mt0) cc_final: 0.7961 (tp40) outliers start: 26 outliers final: 18 residues processed: 296 average time/residue: 0.1099 time to fit residues: 46.3967 Evaluate side-chains 282 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 263 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 125 GLN Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 112 ILE Chi-restraints excluded: chain q residue 62 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 47 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN N 24 GLN N 94 ASN N 110 ASN N 112 GLN P 93 GLN P 113 HIS ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 93 GLN ** p 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 27 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.205812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128341 restraints weight = 21657.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132909 restraints weight = 11558.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135759 restraints weight = 8102.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.137311 restraints weight = 6713.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.138235 restraints weight = 6100.390| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 15174 Z= 0.386 Angle : 1.079 39.877 21681 Z= 0.515 Chirality : 0.052 0.269 2459 Planarity : 0.007 0.069 1791 Dihedral : 28.703 148.109 4242 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.52 % Favored : 97.39 % Rotamer: Outliers : 4.52 % Allowed : 10.65 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1073 helix: 0.64 (0.18), residues: 686 sheet: 1.36 (1.30), residues: 18 loop : -0.67 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG q 55 TYR 0.050 0.004 TYR O 83 PHE 0.036 0.004 PHE o 70 TRP 0.018 0.003 TRP B 34 HIS 0.016 0.003 HIS q 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00834 / 0.38 (15158) covalent geometry : angle 0.93080 / 0.51 (21663) hydrogen bonds : bond 0.08647 / 5.73 ( 892) hydrogen bonds : angle 4.65662 / 3.30 ( 2280) metal coordination : bond 0.03968 / 2.14 ( 16) metal coordination : angle 18.94312 / 13.21 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8957 (mttt) cc_final: 0.8741 (ptpt) REVERT: A 50 LYS cc_start: 0.7930 (mmtt) cc_final: 0.7411 (mmmt) REVERT: A 52 LEU cc_start: 0.8862 (mt) cc_final: 0.8283 (mt) REVERT: A 71 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8036 (mtm-85) REVERT: B 104 MET cc_start: 0.8374 (mmm) cc_final: 0.7993 (mmm) REVERT: N 23 LEU cc_start: 0.9218 (mt) cc_final: 0.8976 (mt) REVERT: N 24 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: N 39 TYR cc_start: 0.9096 (m-80) cc_final: 0.8545 (m-80) REVERT: N 74 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8504 (mmmm) REVERT: N 77 ARG cc_start: 0.7910 (ptp-170) cc_final: 0.7618 (ptp-170) REVERT: N 84 GLN cc_start: 0.8872 (tt0) cc_final: 0.8653 (tt0) REVERT: N 94 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8456 (t0) REVERT: O 59 MET cc_start: 0.8467 (tpp) cc_final: 0.7921 (tpp) REVERT: O 83 TYR cc_start: 0.8063 (m-10) cc_final: 0.7531 (m-10) REVERT: O 84 ASN cc_start: 0.8706 (t0) cc_final: 0.8468 (t0) REVERT: O 99 ARG cc_start: 0.8312 (mtm180) cc_final: 0.8042 (mtm180) REVERT: O 108 LYS cc_start: 0.9093 (mttt) cc_final: 0.8431 (mtpt) REVERT: O 116 LYS cc_start: 0.8654 (ttpp) cc_final: 0.8112 (tttp) REVERT: P 54 TYR cc_start: 0.8037 (m-80) cc_final: 0.7825 (m-80) REVERT: P 73 GLU cc_start: 0.8214 (tp30) cc_final: 0.7680 (tp30) REVERT: P 90 MET cc_start: 0.8028 (mmt) cc_final: 0.7743 (mmt) REVERT: P 100 LEU cc_start: 0.9426 (mt) cc_final: 0.9222 (mt) REVERT: P 125 GLN cc_start: 0.8603 (mt0) cc_final: 0.8291 (mm-40) REVERT: Q 27 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8414 (mm-40) REVERT: n 84 GLN cc_start: 0.8213 (tt0) cc_final: 0.7983 (tt0) REVERT: o 71 GLU cc_start: 0.7430 (tp30) cc_final: 0.7078 (tp30) REVERT: o 99 ARG cc_start: 0.8797 (mtp180) cc_final: 0.8593 (mmm-85) REVERT: p 76 GLN cc_start: 0.8615 (pt0) cc_final: 0.7902 (tp40) REVERT: p 97 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: q 88 TYR cc_start: 0.8922 (m-10) cc_final: 0.8300 (m-80) outliers start: 42 outliers final: 26 residues processed: 324 average time/residue: 0.1340 time to fit residues: 60.4398 Evaluate side-chains 319 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 94 ASN Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 91 GLU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain o residue 90 THR Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 97 GLU Chi-restraints excluded: chain p residue 101 VAL Chi-restraints excluded: chain p residue 112 ILE Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 93 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 94 ASN O 63 ASN O 82 HIS P 85 GLN ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.211032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.134494 restraints weight = 21424.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.139365 restraints weight = 11216.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.142342 restraints weight = 7780.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.144071 restraints weight = 6410.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.144887 restraints weight = 5808.163| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15174 Z= 0.171 Angle : 0.866 36.543 21681 Z= 0.398 Chirality : 0.044 0.332 2459 Planarity : 0.005 0.061 1791 Dihedral : 28.649 147.045 4242 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.77 % Favored : 98.14 % Rotamer: Outliers : 3.76 % Allowed : 15.05 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1073 helix: 1.53 (0.19), residues: 686 sheet: 1.70 (1.34), residues: 18 loop : -0.56 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 92 TYR 0.018 0.002 TYR O 42 PHE 0.025 0.002 PHE o 70 TRP 0.012 0.001 TRP B 34 HIS 0.008 0.001 HIS q 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (15158) covalent geometry : angle 0.66594 / 0.39 (21663) hydrogen bonds : bond 0.06186 / 4.12 ( 892) hydrogen bonds : angle 3.90277 / 2.82 ( 2280) metal coordination : bond 0.02144 / 1.25 ( 16) metal coordination : angle 19.23801 / 13.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 292 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.9161 (t80) cc_final: 0.8899 (t80) REVERT: A 50 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7271 (mmmt) REVERT: A 71 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8079 (mtm-85) REVERT: A 320 VAL cc_start: -0.0558 (OUTLIER) cc_final: -0.0861 (p) REVERT: N 36 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8127 (tttt) REVERT: N 39 TYR cc_start: 0.8954 (m-80) cc_final: 0.8733 (m-80) REVERT: N 42 ARG cc_start: 0.9155 (mtp180) cc_final: 0.8930 (mtp-110) REVERT: N 74 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8491 (mmmm) REVERT: N 94 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8592 (t0) REVERT: O 62 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8536 (mmt) REVERT: O 63 ASN cc_start: 0.8103 (m110) cc_final: 0.7814 (m110) REVERT: O 84 ASN cc_start: 0.8595 (t0) cc_final: 0.8266 (t0) REVERT: O 108 LYS cc_start: 0.8994 (mttt) cc_final: 0.8383 (mtpt) REVERT: O 116 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8101 (tttp) REVERT: P 73 GLU cc_start: 0.8064 (tp30) cc_final: 0.7481 (tp30) REVERT: P 100 LEU cc_start: 0.9386 (mt) cc_final: 0.9051 (mt) REVERT: P 125 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: Q 27 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8394 (mm-40) REVERT: Q 30 THR cc_start: 0.9416 (p) cc_final: 0.8918 (t) REVERT: Q 67 ARG cc_start: 0.8317 (ttm110) cc_final: 0.8090 (ttp-110) REVERT: Q 74 GLU cc_start: 0.8274 (tt0) cc_final: 0.8044 (tt0) REVERT: n 17 ARG cc_start: 0.8290 (mtp180) cc_final: 0.7972 (mtp180) REVERT: n 74 LYS cc_start: 0.9009 (mttt) cc_final: 0.8505 (tttt) REVERT: n 84 GLN cc_start: 0.8101 (tt0) cc_final: 0.7839 (tt0) REVERT: o 71 GLU cc_start: 0.7395 (tp30) cc_final: 0.7099 (tp30) REVERT: p 76 GLN cc_start: 0.8581 (pt0) cc_final: 0.7789 (tp40) REVERT: q 62 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9346 (mp) REVERT: q 88 TYR cc_start: 0.8755 (m-10) cc_final: 0.8196 (m-80) outliers start: 35 outliers final: 21 residues processed: 303 average time/residue: 0.1309 time to fit residues: 55.6213 Evaluate side-chains 303 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 275 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LYS Chi-restraints excluded: chain N residue 94 ASN Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 62 MET Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 125 GLN Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 91 GLU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 52 GLU Chi-restraints excluded: chain q residue 62 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 121 optimal weight: 1.9990 chunk 17 optimal weight: 30.0000 chunk 56 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 77 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 81 GLN ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 94 ASN P 93 GLN ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.211856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134742 restraints weight = 21463.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139659 restraints weight = 11236.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.142599 restraints weight = 7798.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144342 restraints weight = 6449.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.145200 restraints weight = 5857.483| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15174 Z= 0.157 Angle : 0.858 36.268 21681 Z= 0.390 Chirality : 0.043 0.236 2459 Planarity : 0.005 0.062 1791 Dihedral : 28.616 149.401 4242 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.04 % Rotamer: Outliers : 3.76 % Allowed : 16.34 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.25), residues: 1073 helix: 1.76 (0.19), residues: 685 sheet: 1.74 (1.36), residues: 18 loop : -0.53 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 79 TYR 0.025 0.002 TYR o 40 PHE 0.029 0.002 PHE o 70 TRP 0.012 0.001 TRP B 34 HIS 0.006 0.001 HIS p 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (15158) covalent geometry : angle 0.65774 / 0.38 (21663) hydrogen bonds : bond 0.05732 / 3.83 ( 892) hydrogen bonds : angle 3.75663 / 2.73 ( 2280) metal coordination : bond 0.01458 / 0.87 ( 16) metal coordination : angle 19.13403 / 13.56 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 285 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8117 (mtm-85) REVERT: A 320 VAL cc_start: -0.0542 (OUTLIER) cc_final: -0.0864 (p) REVERT: A 347 MET cc_start: 0.4586 (tpp) cc_final: 0.4266 (tpp) REVERT: N 36 LYS cc_start: 0.8450 (tttt) cc_final: 0.8150 (tttt) REVERT: N 39 TYR cc_start: 0.8922 (m-80) cc_final: 0.8700 (m-10) REVERT: N 74 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8504 (mmmm) REVERT: N 94 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8553 (t0) REVERT: N 95 LYS cc_start: 0.8795 (tppp) cc_final: 0.7998 (tptp) REVERT: O 63 ASN cc_start: 0.8116 (m110) cc_final: 0.7868 (m110) REVERT: O 84 ASN cc_start: 0.8611 (t0) cc_final: 0.8275 (t0) REVERT: O 108 LYS cc_start: 0.9008 (mttt) cc_final: 0.8397 (mtpt) REVERT: O 116 LYS cc_start: 0.8752 (ttpp) cc_final: 0.8188 (tttp) REVERT: P 73 GLU cc_start: 0.8022 (tp30) cc_final: 0.7383 (tp30) REVERT: P 100 LEU cc_start: 0.9359 (mt) cc_final: 0.9105 (mt) REVERT: P 125 GLN cc_start: 0.8488 (mt0) cc_final: 0.8043 (mt0) REVERT: Q 27 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8160 (mm-40) REVERT: Q 30 THR cc_start: 0.9390 (p) cc_final: 0.8890 (t) REVERT: Q 44 LYS cc_start: 0.8767 (tttm) cc_final: 0.8156 (ttmm) REVERT: Q 74 GLU cc_start: 0.8269 (tt0) cc_final: 0.8063 (tt0) REVERT: Q 77 LYS cc_start: 0.9127 (mmtm) cc_final: 0.8850 (tppt) REVERT: n 17 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7972 (mtp180) REVERT: n 74 LYS cc_start: 0.9049 (mttt) cc_final: 0.8534 (tttt) REVERT: o 71 GLU cc_start: 0.7423 (tp30) cc_final: 0.7047 (tp30) REVERT: o 93 GLU cc_start: 0.8373 (mp0) cc_final: 0.8110 (mp0) REVERT: p 76 GLN cc_start: 0.8616 (pt0) cc_final: 0.7827 (tp40) REVERT: q 36 ARG cc_start: 0.8771 (mpp80) cc_final: 0.8362 (mpp80) REVERT: q 62 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9270 (mp) REVERT: q 88 TYR cc_start: 0.8727 (m-10) cc_final: 0.8186 (m-80) outliers start: 35 outliers final: 23 residues processed: 298 average time/residue: 0.1094 time to fit residues: 46.5044 Evaluate side-chains 304 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 94 ASN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 82 HIS Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 91 GLU Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 77 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 0.0020 chunk 33 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 94 ASN ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.211050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133930 restraints weight = 21381.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138745 restraints weight = 11224.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141686 restraints weight = 7817.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143362 restraints weight = 6468.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.144142 restraints weight = 5876.742| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15174 Z= 0.167 Angle : 0.855 38.268 21681 Z= 0.388 Chirality : 0.042 0.216 2459 Planarity : 0.005 0.061 1791 Dihedral : 28.606 150.833 4242 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 3.98 % Allowed : 16.88 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.25), residues: 1073 helix: 1.81 (0.19), residues: 682 sheet: 1.78 (1.37), residues: 18 loop : -0.56 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 79 TYR 0.025 0.002 TYR o 40 PHE 0.020 0.002 PHE o 70 TRP 0.011 0.001 TRP B 34 HIS 0.008 0.001 HIS p 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (15158) covalent geometry : angle 0.65439 / 0.37 (21663) hydrogen bonds : bond 0.05544 / 3.70 ( 892) hydrogen bonds : angle 3.76042 / 2.73 ( 2280) metal coordination : bond 0.01358 / 0.81 ( 16) metal coordination : angle 19.13568 / 13.66 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 24 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: N 36 LYS cc_start: 0.8463 (tttt) cc_final: 0.8166 (tttt) REVERT: N 39 TYR cc_start: 0.8915 (m-80) cc_final: 0.8699 (m-10) REVERT: N 56 GLU cc_start: 0.7900 (tt0) cc_final: 0.7423 (tt0) REVERT: N 74 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8519 (mmmm) REVERT: N 94 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8601 (t0) REVERT: O 63 ASN cc_start: 0.8179 (m110) cc_final: 0.7907 (m110) REVERT: O 84 ASN cc_start: 0.8631 (t0) cc_final: 0.8277 (t0) REVERT: O 108 LYS cc_start: 0.9001 (mttt) cc_final: 0.8418 (mtpt) REVERT: O 116 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8215 (tttp) REVERT: P 125 GLN cc_start: 0.8504 (mt0) cc_final: 0.8093 (mt0) REVERT: Q 27 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8151 (mm-40) REVERT: Q 30 THR cc_start: 0.9389 (p) cc_final: 0.8871 (t) REVERT: Q 44 LYS cc_start: 0.8835 (tttm) cc_final: 0.8216 (ttmm) REVERT: Q 74 GLU cc_start: 0.8260 (tt0) cc_final: 0.8033 (tt0) REVERT: Q 84 MET cc_start: 0.7847 (mmt) cc_final: 0.7390 (mmt) REVERT: n 74 LYS cc_start: 0.9062 (mttt) cc_final: 0.8579 (tttt) REVERT: o 59 MET cc_start: 0.7370 (tpp) cc_final: 0.7010 (tpp) REVERT: o 71 GLU cc_start: 0.7345 (tp30) cc_final: 0.7042 (tp30) REVERT: o 99 ARG cc_start: 0.8646 (mtp180) cc_final: 0.8288 (ttm170) REVERT: p 76 GLN cc_start: 0.8657 (pt0) cc_final: 0.7803 (tp40) REVERT: q 88 TYR cc_start: 0.8748 (m-10) cc_final: 0.8162 (m-80) outliers start: 37 outliers final: 25 residues processed: 292 average time/residue: 0.1173 time to fit residues: 48.6466 Evaluate side-chains 300 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 273 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 94 ASN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 82 HIS Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 91 GLU Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 77 LYS Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 94 ASN Q 64 ASN ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.211322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134446 restraints weight = 21397.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.139295 restraints weight = 11274.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.142241 restraints weight = 7850.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.143881 restraints weight = 6495.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144668 restraints weight = 5909.590| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15174 Z= 0.164 Angle : 0.850 39.070 21681 Z= 0.383 Chirality : 0.041 0.222 2459 Planarity : 0.005 0.062 1791 Dihedral : 28.609 152.082 4242 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 3.98 % Allowed : 17.10 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.25), residues: 1073 helix: 1.90 (0.19), residues: 682 sheet: 1.81 (1.39), residues: 18 loop : -0.58 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG p 131 TYR 0.028 0.002 TYR o 40 PHE 0.020 0.002 PHE o 70 TRP 0.011 0.001 TRP B 34 HIS 0.007 0.001 HIS p 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (15158) covalent geometry : angle 0.64750 / 0.37 (21663) hydrogen bonds : bond 0.05369 / 3.58 ( 892) hydrogen bonds : angle 3.74416 / 2.73 ( 2280) metal coordination : bond 0.01190 / 0.71 ( 16) metal coordination : angle 19.10913 / 13.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.4350 (tpp) cc_final: 0.4052 (tpp) REVERT: N 36 LYS cc_start: 0.8474 (tttt) cc_final: 0.8165 (tttt) REVERT: N 39 TYR cc_start: 0.8874 (m-80) cc_final: 0.8671 (m-10) REVERT: N 74 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8553 (mmmm) REVERT: N 94 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8629 (t0) REVERT: O 59 MET cc_start: 0.8204 (tpp) cc_final: 0.7579 (tpp) REVERT: O 63 ASN cc_start: 0.8168 (m110) cc_final: 0.7902 (m110) REVERT: O 84 ASN cc_start: 0.8648 (t0) cc_final: 0.8268 (t0) REVERT: O 108 LYS cc_start: 0.9008 (mttt) cc_final: 0.8431 (mtpt) REVERT: O 116 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8217 (tttp) REVERT: P 109 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7947 (tt) REVERT: P 125 GLN cc_start: 0.8492 (mt0) cc_final: 0.8071 (mt0) REVERT: Q 27 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8182 (mm-40) REVERT: Q 30 THR cc_start: 0.9358 (p) cc_final: 0.8848 (t) REVERT: Q 74 GLU cc_start: 0.8230 (tt0) cc_final: 0.8021 (tt0) REVERT: Q 84 MET cc_start: 0.7849 (mmt) cc_final: 0.7388 (mmt) REVERT: n 73 ASN cc_start: 0.8697 (m-40) cc_final: 0.8460 (t0) REVERT: n 74 LYS cc_start: 0.9045 (mttt) cc_final: 0.8592 (tttt) REVERT: o 71 GLU cc_start: 0.7348 (tp30) cc_final: 0.7033 (tp30) REVERT: o 93 GLU cc_start: 0.8304 (mp0) cc_final: 0.7934 (mp0) REVERT: o 99 ARG cc_start: 0.8660 (mtp180) cc_final: 0.8273 (ttm170) REVERT: p 76 GLN cc_start: 0.8657 (pt0) cc_final: 0.7837 (tp40) REVERT: p 131 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8353 (ttm-80) outliers start: 37 outliers final: 29 residues processed: 300 average time/residue: 0.1130 time to fit residues: 48.0381 Evaluate side-chains 310 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 94 ASN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 82 HIS Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain o residue 90 THR Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 77 LYS Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 100 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 94 ASN Q 64 ASN ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.211907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.135156 restraints weight = 21449.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139927 restraints weight = 11286.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142932 restraints weight = 7874.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144551 restraints weight = 6513.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.145331 restraints weight = 5937.998| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15174 Z= 0.151 Angle : 0.846 37.781 21681 Z= 0.380 Chirality : 0.042 0.328 2459 Planarity : 0.004 0.062 1791 Dihedral : 28.593 153.051 4242 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.86 % Rotamer: Outliers : 4.09 % Allowed : 18.06 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.25), residues: 1073 helix: 1.93 (0.19), residues: 685 sheet: 1.94 (1.40), residues: 18 loop : -0.59 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG p 131 TYR 0.028 0.002 TYR o 40 PHE 0.018 0.002 PHE A 46 TRP 0.010 0.001 TRP B 34 HIS 0.008 0.001 HIS q 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (15158) covalent geometry : angle 0.64322 / 0.37 (21663) hydrogen bonds : bond 0.05211 / 3.47 ( 892) hydrogen bonds : angle 3.69691 / 2.69 ( 2280) metal coordination : bond 0.01064 / 0.65 ( 16) metal coordination : angle 19.05952 / 13.53 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.9292 (pm20) cc_final: 0.8858 (pm20) REVERT: A 347 MET cc_start: 0.4295 (tpp) cc_final: 0.3982 (tpp) REVERT: N 36 LYS cc_start: 0.8470 (tttt) cc_final: 0.8184 (tttt) REVERT: N 74 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8558 (mmmm) REVERT: N 94 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8631 (t0) REVERT: O 59 MET cc_start: 0.8184 (tpp) cc_final: 0.7699 (tpp) REVERT: O 84 ASN cc_start: 0.8639 (t0) cc_final: 0.8275 (t0) REVERT: O 108 LYS cc_start: 0.8957 (mttt) cc_final: 0.8367 (mtpt) REVERT: O 116 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8233 (tttp) REVERT: P 109 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7953 (tt) REVERT: P 125 GLN cc_start: 0.8495 (mt0) cc_final: 0.8070 (mt0) REVERT: Q 27 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8111 (mm-40) REVERT: Q 35 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.7761 (mtp85) REVERT: Q 59 LYS cc_start: 0.8803 (tptm) cc_final: 0.8346 (tmtt) REVERT: Q 74 GLU cc_start: 0.8267 (tt0) cc_final: 0.8045 (tt0) REVERT: n 73 ASN cc_start: 0.8652 (m-40) cc_final: 0.8422 (t0) REVERT: n 74 LYS cc_start: 0.9047 (mttt) cc_final: 0.8547 (tttt) REVERT: o 47 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7588 (tt0) REVERT: o 71 GLU cc_start: 0.7286 (tp30) cc_final: 0.6993 (tp30) REVERT: o 93 GLU cc_start: 0.8213 (mp0) cc_final: 0.7836 (mp0) REVERT: o 99 ARG cc_start: 0.8610 (mtp180) cc_final: 0.8273 (ttm170) REVERT: p 76 GLN cc_start: 0.8674 (pt0) cc_final: 0.7841 (tp40) REVERT: p 131 ARG cc_start: 0.8557 (ttm-80) cc_final: 0.8309 (ttm-80) outliers start: 38 outliers final: 31 residues processed: 297 average time/residue: 0.1340 time to fit residues: 56.2091 Evaluate side-chains 309 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 94 ASN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 82 HIS Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 90 MET Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 91 GLU Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 77 LYS Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** 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 = 0.4328 r_free = 0.4328 target = 0.211567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134701 restraints weight = 21632.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.139546 restraints weight = 11357.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142477 restraints weight = 7910.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.144190 restraints weight = 6545.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.145058 restraints weight = 5951.635| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 15174 Z= 0.166 Angle : 0.858 40.902 21681 Z= 0.385 Chirality : 0.041 0.250 2459 Planarity : 0.005 0.061 1791 Dihedral : 28.606 154.228 4242 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 3.87 % Allowed : 18.49 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.25), residues: 1073 helix: 1.91 (0.19), residues: 685 sheet: 1.96 (1.39), residues: 18 loop : -0.57 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG p 131 TYR 0.030 0.002 TYR o 40 PHE 0.013 0.002 PHE P 67 TRP 0.010 0.001 TRP B 34 HIS 0.013 0.001 HIS B 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (15158) covalent geometry : angle 0.65757 / 0.37 (21663) hydrogen bonds : bond 0.05233 / 3.47 ( 892) hydrogen bonds : angle 3.71832 / 2.70 ( 2280) metal coordination : bond 0.01029 / 0.62 ( 16) metal coordination : angle 19.15395 / 13.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 36 LYS cc_start: 0.8469 (tttt) cc_final: 0.8191 (tttt) REVERT: N 39 TYR cc_start: 0.8672 (m-10) cc_final: 0.8043 (m-10) REVERT: N 42 ARG cc_start: 0.9334 (mtp-110) cc_final: 0.8859 (mtp-110) REVERT: N 74 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8582 (mmmm) REVERT: O 59 MET cc_start: 0.8068 (tpp) cc_final: 0.7624 (tpp) REVERT: O 71 GLU cc_start: 0.8409 (tp30) cc_final: 0.8033 (tp30) REVERT: O 84 ASN cc_start: 0.8657 (t0) cc_final: 0.8266 (t0) REVERT: O 108 LYS cc_start: 0.8959 (mttt) cc_final: 0.8368 (mtpt) REVERT: O 116 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8199 (tttp) REVERT: P 109 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7940 (tt) REVERT: P 125 GLN cc_start: 0.8513 (mt0) cc_final: 0.8090 (mt0) REVERT: Q 27 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8206 (mm-40) REVERT: Q 30 THR cc_start: 0.9371 (p) cc_final: 0.8871 (t) REVERT: Q 59 LYS cc_start: 0.8784 (tptm) cc_final: 0.8386 (tptp) REVERT: Q 74 GLU cc_start: 0.8291 (tt0) cc_final: 0.8081 (tt0) REVERT: n 73 ASN cc_start: 0.8634 (m-40) cc_final: 0.8417 (t0) REVERT: n 74 LYS cc_start: 0.9080 (mttt) cc_final: 0.8581 (tttt) REVERT: o 71 GLU cc_start: 0.7309 (tp30) cc_final: 0.6994 (tp30) REVERT: o 93 GLU cc_start: 0.8208 (mp0) cc_final: 0.7850 (mp0) REVERT: o 99 ARG cc_start: 0.8649 (mtp180) cc_final: 0.8270 (ttm170) REVERT: p 76 GLN cc_start: 0.8679 (pt0) cc_final: 0.7863 (tp40) outliers start: 36 outliers final: 32 residues processed: 295 average time/residue: 0.1350 time to fit residues: 56.3630 Evaluate side-chains 313 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 280 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 94 ASN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 90 MET Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 91 GLU Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain o residue 90 THR Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 94 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 82 optimal weight: 40.0000 chunk 78 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 84 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 24 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.208128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130146 restraints weight = 21276.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.134758 restraints weight = 11344.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137630 restraints weight = 7995.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.139222 restraints weight = 6661.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.140000 restraints weight = 6083.490| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15174 Z= 0.215 Angle : 0.888 41.606 21681 Z= 0.402 Chirality : 0.043 0.261 2459 Planarity : 0.005 0.063 1791 Dihedral : 28.705 156.776 4242 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 3.55 % Allowed : 18.92 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1073 helix: 1.78 (0.20), residues: 679 sheet: 1.87 (1.41), residues: 18 loop : -0.61 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG p 131 TYR 0.031 0.002 TYR o 40 PHE 0.021 0.002 PHE o 70 TRP 0.014 0.002 TRP A 293 HIS 0.008 0.002 HIS p 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (15158) covalent geometry : angle 0.69808 / 0.39 (21663) hydrogen bonds : bond 0.05501 / 3.68 ( 892) hydrogen bonds : angle 3.97040 / 2.87 ( 2280) metal coordination : bond 0.01103 / 0.65 ( 16) metal coordination : angle 19.04835 / 13.66 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.9324 (pm20) cc_final: 0.8896 (pm20) REVERT: N 36 LYS cc_start: 0.8525 (tttt) cc_final: 0.8270 (tttt) REVERT: N 39 TYR cc_start: 0.8612 (m-10) cc_final: 0.8098 (m-10) REVERT: N 61 GLU cc_start: 0.8396 (tp30) cc_final: 0.8114 (tp30) REVERT: N 74 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8588 (mmmm) REVERT: N 95 LYS cc_start: 0.8921 (tppp) cc_final: 0.7988 (tptp) REVERT: O 63 ASN cc_start: 0.8143 (m110) cc_final: 0.7736 (p0) REVERT: O 84 ASN cc_start: 0.8687 (t0) cc_final: 0.8344 (t0) REVERT: O 108 LYS cc_start: 0.9003 (mttt) cc_final: 0.8408 (mtpt) REVERT: P 109 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8007 (tt) REVERT: P 125 GLN cc_start: 0.8538 (mt0) cc_final: 0.8139 (mt0) REVERT: Q 27 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8441 (mm-40) REVERT: Q 30 THR cc_start: 0.9426 (p) cc_final: 0.8900 (t) REVERT: Q 59 LYS cc_start: 0.8801 (tptm) cc_final: 0.8372 (tptp) REVERT: Q 84 MET cc_start: 0.8239 (mmt) cc_final: 0.7802 (mmt) REVERT: n 73 ASN cc_start: 0.8629 (m-40) cc_final: 0.8150 (t0) REVERT: n 74 LYS cc_start: 0.9105 (mttt) cc_final: 0.8645 (tttt) REVERT: o 47 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7542 (tt0) REVERT: o 71 GLU cc_start: 0.7471 (tp30) cc_final: 0.7241 (tp30) REVERT: o 93 GLU cc_start: 0.8248 (mp0) cc_final: 0.7856 (mp0) REVERT: p 76 GLN cc_start: 0.8714 (pt0) cc_final: 0.7936 (tp40) REVERT: p 131 ARG cc_start: 0.8549 (ttm-80) cc_final: 0.8320 (ttm-80) outliers start: 33 outliers final: 30 residues processed: 297 average time/residue: 0.1359 time to fit residues: 56.7983 Evaluate side-chains 313 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 282 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 90 MET Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain n residue 18 SER Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 58 LEU Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain o residue 90 THR Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 26 ILE Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 65 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 83 optimal weight: 50.0000 chunk 91 optimal weight: 10.0000 chunk 29 optimal weight: 0.1980 chunk 71 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 24 GLN N 94 ASN ** P 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** 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 = 0.4318 r_free = 0.4318 target = 0.210650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.133832 restraints weight = 21343.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138644 restraints weight = 11183.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141581 restraints weight = 7783.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.143269 restraints weight = 6437.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.144084 restraints weight = 5857.366| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 15174 Z= 0.152 Angle : 0.857 39.814 21681 Z= 0.384 Chirality : 0.041 0.226 2459 Planarity : 0.005 0.061 1791 Dihedral : 28.657 157.163 4242 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.86 % Rotamer: Outliers : 3.33 % Allowed : 19.57 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.26), residues: 1073 helix: 1.80 (0.20), residues: 687 sheet: 1.88 (1.41), residues: 18 loop : -0.52 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG p 131 TYR 0.029 0.002 TYR o 40 PHE 0.012 0.002 PHE Q 61 TRP 0.011 0.001 TRP A 293 HIS 0.007 0.001 HIS p 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (15158) covalent geometry : angle 0.65658 / 0.37 (21663) hydrogen bonds : bond 0.05043 / 3.37 ( 892) hydrogen bonds : angle 3.80576 / 2.77 ( 2280) metal coordination : bond 0.00977 / 0.59 ( 16) metal coordination : angle 19.11008 / 13.56 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2508.66 seconds wall clock time: 43 minutes 53.40 seconds (2633.40 seconds total)