Starting phenix.real_space_refine on Sat Sep 12 05:06:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jzv_22581/09_2026/7jzv_22581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzv_22581/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7jzv_22581/09_2026/7jzv_22581.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jzv_22581/09_2026/7jzv_22581.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jzv_22581/09_2026/7jzv_22581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzv_22581/09_2026/7jzv_22581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jzv_22581/09_2026/7jzv_22581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzv_22581/09_2026/7jzv_22581.map" } 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-2.2.1-6174/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: 3.05, per 1000 atoms: 0.21 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: 0.96 Conformation dependent library (CDL) restraints added in 504.3 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: 1.50 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: 2.38 Time building geometry restraints manager: 1.38 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: 1296 4.84 - 7.26: 264 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.990 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- 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= 0.808 Angle : 1.375 12.099 21681 Z= 1.136 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 / 0.81 (15158) covalent geometry : angle 1.37433 / 1.14 (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 : 0.337 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: 0.5317 (tt0) REVERT: A 25 PRO cc_start: 0.7787 (Cg_exo) cc_final: 0.7281 (Cg_endo) REVERT: A 52 LEU cc_start: 0.7041 (mt) cc_final: 0.5728 (mt) REVERT: N 39 TYR cc_start: 0.8373 (m-80) cc_final: 0.8002 (m-80) REVERT: O 36 SER cc_start: 0.8125 (p) cc_final: 0.7795 (m) REVERT: O 108 LYS cc_start: 0.7870 (mttt) cc_final: 0.7266 (mtpt) REVERT: P 60 LEU cc_start: 0.7035 (mt) cc_final: 0.6765 (mt) REVERT: Q 52 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6912 (mm-30) REVERT: Q 53 GLU cc_start: 0.7836 (tp30) cc_final: 0.7451 (tp30) REVERT: p 60 LEU cc_start: 0.8272 (mt) cc_final: 0.7721 (mt) outliers start: 2 outliers final: 0 residues processed: 329 average time/residue: 0.1333 time to fit residues: 60.6554 Evaluate side-chains 254 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.221734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149913 restraints weight = 21844.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.155058 restraints weight = 11140.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.158234 restraints weight = 7622.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.160038 restraints weight = 6237.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.160894 restraints weight = 5642.372| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15174 Z= 0.202 Angle : 0.987 41.919 21681 Z= 0.462 Chirality : 0.051 0.279 2459 Planarity : 0.005 0.045 1791 Dihedral : 27.944 146.972 4242 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.49 % Favored : 98.42 % Rotamer: Outliers : 2.90 % Allowed : 8.39 % Favored : 88.71 % 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: 1.53 (0.24), residues: 1073 helix: 1.74 (0.19), residues: 678 sheet: 0.18 (1.23), residues: 18 loop : -0.23 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 86 TYR 0.029 0.002 TYR B 87 PHE 0.020 0.003 PHE P 67 TRP 0.015 0.002 TRP A 293 HIS 0.011 0.002 HIS B 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.20 (15158) covalent geometry : angle 0.78599 / 0.45 (21663) hydrogen bonds : bond 0.09565 / 6.28 ( 892) hydrogen bonds : angle 4.11211 / 2.95 ( 2280) metal coordination : bond 0.02418 / 1.54 ( 16) metal coordination : angle 20.70517 / 14.72 ( 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 319 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 292 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8924 (tpp) cc_final: 0.8683 (tpp) REVERT: A 52 LEU cc_start: 0.8732 (mt) cc_final: 0.8222 (mt) REVERT: A 71 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7955 (mtm110) REVERT: A 81 GLN cc_start: 0.9085 (mt0) cc_final: 0.8707 (pt0) REVERT: B 104 MET cc_start: 0.8171 (mmm) cc_final: 0.7817 (mmm) REVERT: N 23 LEU cc_start: 0.8977 (mt) cc_final: 0.8645 (mt) REVERT: N 95 LYS cc_start: 0.8901 (tppt) cc_final: 0.7870 (tptt) REVERT: O 36 SER cc_start: 0.8517 (p) cc_final: 0.8269 (m) REVERT: O 86 ARG cc_start: 0.7992 (mmt90) cc_final: 0.7449 (mmt90) REVERT: O 108 LYS cc_start: 0.8844 (mttt) cc_final: 0.8191 (mtpt) REVERT: O 116 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8006 (tttp) REVERT: P 93 GLN cc_start: 0.8820 (tt0) cc_final: 0.8601 (tt0) REVERT: Q 52 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7799 (mm-30) REVERT: Q 74 GLU cc_start: 0.8175 (tt0) cc_final: 0.7848 (tt0) REVERT: n 84 GLN cc_start: 0.8095 (tt0) cc_final: 0.7795 (tt0) REVERT: n 88 ARG cc_start: 0.7622 (mmt180) cc_final: 0.7290 (tpp80) REVERT: p 125 GLN cc_start: 0.8277 (mt0) cc_final: 0.7956 (tp40) REVERT: q 36 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8523 (mpp80) outliers start: 27 outliers final: 17 residues processed: 299 average time/residue: 0.1247 time to fit residues: 53.0102 Evaluate side-chains 286 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 268 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 9 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 47 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 overall best weight: 3.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN N 24 GLN N 94 ASN P 93 GLN P 113 HIS ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 93 GLN q 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.207945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.130611 restraints weight = 21662.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135269 restraints weight = 11522.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.138124 restraints weight = 8067.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.139651 restraints weight = 6675.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.140481 restraints weight = 6070.897| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 15174 Z= 0.360 Angle : 1.023 41.270 21681 Z= 0.484 Chirality : 0.050 0.270 2459 Planarity : 0.006 0.058 1791 Dihedral : 28.463 146.831 4242 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 3.98 % Allowed : 10.54 % Favored : 85.48 % 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: 0.67 (0.24), residues: 1073 helix: 1.04 (0.19), residues: 686 sheet: 1.04 (1.28), residues: 18 loop : -0.60 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 36 TYR 0.025 0.003 TYR O 83 PHE 0.030 0.003 PHE o 70 TRP 0.017 0.002 TRP B 34 HIS 0.013 0.003 HIS q 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.36 (15158) covalent geometry : angle 0.85742 / 0.47 (21663) hydrogen bonds : bond 0.08261 / 5.45 ( 892) hydrogen bonds : angle 4.42132 / 3.15 ( 2280) metal coordination : bond 0.03437 / 2.18 ( 16) metal coordination : angle 19.40506 / 13.42 ( 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 336 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 0.403 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 45 LYS cc_start: 0.8931 (mttt) cc_final: 0.8555 (mttt) REVERT: A 50 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7386 (mmmt) REVERT: A 52 LEU cc_start: 0.8842 (mt) cc_final: 0.8254 (mt) REVERT: A 71 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8112 (mtm-85) REVERT: B 104 MET cc_start: 0.8363 (mmm) cc_final: 0.7993 (mmm) REVERT: N 24 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: N 39 TYR cc_start: 0.9082 (m-80) cc_final: 0.8558 (m-80) REVERT: N 74 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8496 (mmmm) REVERT: N 94 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8344 (t0) REVERT: N 102 ILE cc_start: 0.9169 (mm) cc_final: 0.8923 (tp) REVERT: O 84 ASN cc_start: 0.8725 (t0) cc_final: 0.8423 (t0) REVERT: O 99 ARG cc_start: 0.8432 (mtm180) cc_final: 0.8155 (mtm180) REVERT: O 108 LYS cc_start: 0.9051 (mttt) cc_final: 0.8444 (mtpt) REVERT: O 116 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8107 (tttp) REVERT: P 100 LEU cc_start: 0.9404 (mt) cc_final: 0.9135 (mt) REVERT: Q 27 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8103 (mm-40) REVERT: Q 44 LYS cc_start: 0.8912 (tttm) cc_final: 0.8702 (tttm) REVERT: o 71 GLU cc_start: 0.7434 (tp30) cc_final: 0.7115 (tp30) REVERT: p 76 GLN cc_start: 0.8602 (pt0) cc_final: 0.7915 (tp40) REVERT: q 36 ARG cc_start: 0.9019 (mtm-85) cc_final: 0.8675 (mpp80) REVERT: q 88 TYR cc_start: 0.8945 (m-10) cc_final: 0.8380 (m-80) outliers start: 37 outliers final: 25 residues processed: 312 average time/residue: 0.1406 time to fit residues: 61.3425 Evaluate side-chains 312 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 284 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 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 54 THR Chi-restraints excluded: chain Q residue 80 THR 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 67 ASN 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: 10.0000 chunk 15 optimal weight: 30.0000 chunk 127 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 93 GLN ** p 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.213060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.136257 restraints weight = 21472.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141114 restraints weight = 11254.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144120 restraints weight = 7812.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.145805 restraints weight = 6456.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.146611 restraints weight = 5862.019| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3811 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= 0.165 Angle : 0.868 37.714 21681 Z= 0.398 Chirality : 0.044 0.283 2459 Planarity : 0.005 0.059 1791 Dihedral : 28.434 146.174 4242 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.77 % Favored : 98.14 % Rotamer: Outliers : 3.87 % Allowed : 13.23 % Favored : 82.90 % 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: 1.38 (0.25), residues: 1073 helix: 1.65 (0.19), residues: 687 sheet: 1.49 (1.32), residues: 18 loop : -0.47 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 92 TYR 0.021 0.002 TYR B 87 PHE 0.022 0.002 PHE o 70 TRP 0.013 0.001 TRP B 34 HIS 0.008 0.001 HIS q 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (15158) covalent geometry : angle 0.66698 / 0.38 (21663) hydrogen bonds : bond 0.06327 / 4.21 ( 892) hydrogen bonds : angle 3.82898 / 2.77 ( 2280) metal coordination : bond 0.02081 / 1.24 ( 16) metal coordination : angle 19.30025 / 13.63 ( 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 329 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8871 (mttt) cc_final: 0.8516 (mttt) REVERT: A 46 PHE cc_start: 0.9169 (t80) cc_final: 0.8914 (t80) REVERT: A 50 LYS cc_start: 0.7817 (mmtt) cc_final: 0.7272 (mmmt) REVERT: A 71 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7994 (mtm-85) REVERT: A 81 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8614 (pp30) REVERT: A 320 VAL cc_start: -0.0283 (OUTLIER) cc_final: -0.0629 (p) REVERT: A 347 MET cc_start: 0.4491 (tpp) cc_final: 0.4114 (tpp) REVERT: N 23 LEU cc_start: 0.9100 (mt) cc_final: 0.8687 (mp) REVERT: N 24 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: N 36 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8109 (tttt) REVERT: N 39 TYR cc_start: 0.8998 (m-80) cc_final: 0.8708 (m-80) REVERT: N 74 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8462 (mmmm) REVERT: N 94 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8598 (t0) REVERT: O 63 ASN cc_start: 0.8038 (m110) cc_final: 0.7778 (m110) REVERT: O 83 TYR cc_start: 0.7541 (m-10) cc_final: 0.7232 (m-10) REVERT: O 84 ASN cc_start: 0.8601 (t0) cc_final: 0.7638 (t0) REVERT: O 86 ARG cc_start: 0.8017 (mmt90) cc_final: 0.7196 (mmt90) REVERT: O 108 LYS cc_start: 0.9008 (mttt) cc_final: 0.8384 (mtpt) REVERT: O 116 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8113 (tttp) REVERT: P 100 LEU cc_start: 0.9347 (mt) cc_final: 0.9020 (mt) REVERT: Q 67 ARG cc_start: 0.8325 (ttm110) cc_final: 0.8097 (ttp-110) REVERT: Q 74 GLU cc_start: 0.8268 (tt0) cc_final: 0.8033 (tt0) REVERT: Q 84 MET cc_start: 0.8111 (mmt) cc_final: 0.7532 (mmt) REVERT: n 74 LYS cc_start: 0.9004 (mttt) cc_final: 0.8432 (tttt) REVERT: o 93 GLU cc_start: 0.8449 (mp0) cc_final: 0.8087 (mp0) REVERT: p 76 GLN cc_start: 0.8519 (pt0) cc_final: 0.7782 (tp40) REVERT: q 88 TYR cc_start: 0.8761 (m-10) cc_final: 0.8189 (m-80) outliers start: 36 outliers final: 22 residues processed: 306 average time/residue: 0.1310 time to fit residues: 57.0530 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 : 0.401 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain N residue 84 GLN 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 105 GLU 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 96 SER Chi-restraints excluded: chain P residue 124 ILE 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 66 VAL Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 52 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 121 optimal weight: 0.5980 chunk 17 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.0000 chunk 77 optimal weight: 10.0000 chunk 29 optimal weight: 40.0000 chunk 64 optimal weight: 0.9980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 P 113 HIS P 125 GLN ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 93 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.213650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.136418 restraints weight = 21572.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141360 restraints weight = 11272.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.144417 restraints weight = 7808.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.146106 restraints weight = 6433.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146837 restraints weight = 5844.489| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15174 Z= 0.154 Angle : 0.856 36.860 21681 Z= 0.389 Chirality : 0.043 0.233 2459 Planarity : 0.005 0.060 1791 Dihedral : 28.431 148.177 4242 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.04 % Rotamer: Outliers : 3.55 % Allowed : 15.48 % Favored : 80.97 % 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: 1.56 (0.25), residues: 1073 helix: 1.85 (0.19), residues: 685 sheet: 1.67 (1.36), residues: 18 loop : -0.54 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG n 35 TYR 0.019 0.002 TYR B 87 PHE 0.029 0.002 PHE o 70 TRP 0.012 0.001 TRP B 34 HIS 0.013 0.001 HIS n 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (15158) covalent geometry : angle 0.65514 / 0.38 (21663) hydrogen bonds : bond 0.05907 / 3.93 ( 892) hydrogen bonds : angle 3.76711 / 2.74 ( 2280) metal coordination : bond 0.01480 / 0.89 ( 16) metal coordination : angle 19.14680 / 13.48 ( 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 311 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8859 (mttt) cc_final: 0.8455 (mttt) REVERT: A 71 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8120 (mtm-85) REVERT: A 320 VAL cc_start: -0.0535 (OUTLIER) cc_final: -0.0856 (p) REVERT: A 347 MET cc_start: 0.4628 (tpp) cc_final: 0.4318 (tpp) REVERT: N 36 LYS cc_start: 0.8463 (tttt) cc_final: 0.8153 (tttt) REVERT: N 39 TYR cc_start: 0.8986 (m-80) cc_final: 0.8434 (m-10) REVERT: N 74 LYS cc_start: 0.8747 (mmtt) cc_final: 0.8504 (mmmm) REVERT: N 95 LYS cc_start: 0.8825 (tppp) cc_final: 0.7900 (tptp) REVERT: O 63 ASN cc_start: 0.8067 (m110) cc_final: 0.7788 (m110) REVERT: O 71 GLU cc_start: 0.8409 (tp30) cc_final: 0.8057 (tp30) REVERT: O 83 TYR cc_start: 0.7554 (m-10) cc_final: 0.7201 (m-10) REVERT: O 84 ASN cc_start: 0.8630 (t0) cc_final: 0.7626 (t0) REVERT: O 86 ARG cc_start: 0.8130 (mmt90) cc_final: 0.7221 (mmt90) REVERT: O 92 ARG cc_start: 0.7630 (mtp85) cc_final: 0.7281 (mtp85) REVERT: O 108 LYS cc_start: 0.9004 (mttt) cc_final: 0.8360 (mtpt) REVERT: O 116 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8144 (tttp) REVERT: P 100 LEU cc_start: 0.9319 (mt) cc_final: 0.9044 (mt) REVERT: Q 27 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8054 (mm-40) REVERT: Q 67 ARG cc_start: 0.8357 (ttm110) cc_final: 0.8117 (ttp-110) REVERT: Q 74 GLU cc_start: 0.8258 (tt0) cc_final: 0.8022 (tt0) REVERT: Q 84 MET cc_start: 0.8126 (mmt) cc_final: 0.7886 (mmt) REVERT: n 17 ARG cc_start: 0.8250 (mtp180) cc_final: 0.8045 (mtp180) REVERT: n 35 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.7049 (mtm-85) REVERT: n 74 LYS cc_start: 0.9022 (mttt) cc_final: 0.8435 (tttt) REVERT: o 93 GLU cc_start: 0.8498 (mp0) cc_final: 0.8220 (mp0) REVERT: p 76 GLN cc_start: 0.8586 (pt0) cc_final: 0.7836 (tp40) REVERT: q 88 TYR cc_start: 0.8750 (m-10) cc_final: 0.8109 (m-80) outliers start: 33 outliers final: 20 residues processed: 290 average time/residue: 0.1271 time to fit residues: 52.5085 Evaluate side-chains 289 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 267 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 76 THR 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 92 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 124 ILE 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 p residue 46 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 73 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 81 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 HIS P 125 GLN ** 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 = 0.4312 r_free = 0.4312 target = 0.209408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131836 restraints weight = 21320.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.136519 restraints weight = 11289.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.139469 restraints weight = 7903.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141119 restraints weight = 6537.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141966 restraints weight = 5938.997| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15174 Z= 0.215 Angle : 0.886 37.156 21681 Z= 0.404 Chirality : 0.044 0.360 2459 Planarity : 0.005 0.063 1791 Dihedral : 28.521 150.085 4242 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.86 % Rotamer: Outliers : 4.84 % Allowed : 15.70 % Favored : 79.46 % 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: 1.48 (0.25), residues: 1073 helix: 1.80 (0.19), residues: 682 sheet: 1.77 (1.37), residues: 18 loop : -0.58 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG n 35 TYR 0.018 0.002 TYR O 83 PHE 0.035 0.003 PHE o 70 TRP 0.011 0.001 TRP B 34 HIS 0.013 0.001 HIS n 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (15158) covalent geometry : angle 0.69545 / 0.39 (21663) hydrogen bonds : bond 0.05856 / 3.90 ( 892) hydrogen bonds : angle 3.90604 / 2.83 ( 2280) metal coordination : bond 0.01503 / 0.84 ( 16) metal coordination : angle 19.05371 / 13.57 ( 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 328 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 283 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8065 (mtm-85) REVERT: N 36 LYS cc_start: 0.8469 (tttt) cc_final: 0.8118 (tttt) REVERT: N 39 TYR cc_start: 0.8984 (m-80) cc_final: 0.8778 (m-10) REVERT: N 74 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8556 (mmmm) REVERT: N 94 ASN cc_start: 0.8788 (t0) cc_final: 0.8584 (t0) REVERT: O 83 TYR cc_start: 0.7682 (m-10) cc_final: 0.7205 (m-10) REVERT: O 84 ASN cc_start: 0.8619 (t0) cc_final: 0.8089 (t0) REVERT: O 108 LYS cc_start: 0.9068 (mttt) cc_final: 0.8451 (mtpt) REVERT: O 116 LYS cc_start: 0.8700 (ttpp) cc_final: 0.8162 (tttp) REVERT: P 100 LEU cc_start: 0.9394 (mt) cc_final: 0.9080 (mt) REVERT: P 125 GLN cc_start: 0.8533 (mt0) cc_final: 0.8306 (mt0) REVERT: Q 27 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8155 (mm-40) REVERT: Q 30 THR cc_start: 0.9420 (p) cc_final: 0.8888 (t) REVERT: Q 62 LEU cc_start: 0.9453 (mt) cc_final: 0.9206 (mm) REVERT: Q 67 ARG cc_start: 0.8364 (ttm110) cc_final: 0.8148 (ttp-110) REVERT: Q 74 GLU cc_start: 0.8317 (tt0) cc_final: 0.8067 (tt0) REVERT: n 73 ASN cc_start: 0.8833 (t0) cc_final: 0.8440 (t0) REVERT: n 74 LYS cc_start: 0.9025 (mttt) cc_final: 0.8498 (tttt) REVERT: o 93 GLU cc_start: 0.8547 (mp0) cc_final: 0.8277 (mp0) REVERT: p 76 GLN cc_start: 0.8657 (pt0) cc_final: 0.7894 (tp40) REVERT: q 88 TYR cc_start: 0.8714 (m-10) cc_final: 0.8191 (m-80) outliers start: 45 outliers final: 32 residues processed: 300 average time/residue: 0.1236 time to fit residues: 52.6524 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 : 0.334 ------------------------------------------------------------------------------- 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 74 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 76 THR 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 74 ILE 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 124 ILE 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 39 VAL Chi-restraints excluded: chain o residue 66 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 p residue 112 ILE Chi-restraints excluded: chain q residue 73 THR 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: 0.4980 chunk 85 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 108 optimal weight: 0.0670 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.212766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135267 restraints weight = 21517.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.140069 restraints weight = 11351.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.143116 restraints weight = 7928.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144821 restraints weight = 6559.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.145477 restraints weight = 5959.441| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15174 Z= 0.152 Angle : 0.858 38.050 21681 Z= 0.387 Chirality : 0.042 0.218 2459 Planarity : 0.004 0.063 1791 Dihedral : 28.486 150.584 4242 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 3.76 % Allowed : 17.53 % Favored : 78.71 % 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: 1.60 (0.25), residues: 1073 helix: 1.94 (0.19), residues: 684 sheet: 1.78 (1.37), residues: 18 loop : -0.63 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG n 35 TYR 0.015 0.002 TYR O 42 PHE 0.017 0.002 PHE Q 100 TRP 0.010 0.001 TRP B 34 HIS 0.013 0.001 HIS n 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (15158) covalent geometry : angle 0.65819 / 0.37 (21663) hydrogen bonds : bond 0.05388 / 3.59 ( 892) hydrogen bonds : angle 3.76002 / 2.75 ( 2280) metal coordination : bond 0.01219 / 0.73 ( 16) metal coordination : angle 19.13686 / 13.64 ( 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 319 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8048 (mtm-85) REVERT: A 347 MET cc_start: 0.4394 (tpp) cc_final: 0.4077 (tpp) REVERT: N 24 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: N 36 LYS cc_start: 0.8454 (tttt) cc_final: 0.8107 (tttt) REVERT: N 39 TYR cc_start: 0.8929 (m-80) cc_final: 0.8719 (m-10) REVERT: N 56 GLU cc_start: 0.7836 (tt0) cc_final: 0.7505 (tt0) REVERT: N 74 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8554 (mmmm) REVERT: N 95 LYS cc_start: 0.8907 (tppp) cc_final: 0.8116 (tptp) REVERT: O 63 ASN cc_start: 0.8035 (m110) cc_final: 0.7821 (m110) REVERT: O 83 TYR cc_start: 0.7669 (m-10) cc_final: 0.7189 (m-10) REVERT: O 84 ASN cc_start: 0.8671 (t0) cc_final: 0.7529 (t0) REVERT: O 86 ARG cc_start: 0.8134 (mmt90) cc_final: 0.7218 (mmt90) REVERT: O 108 LYS cc_start: 0.9003 (mttt) cc_final: 0.8399 (mtpt) REVERT: O 116 LYS cc_start: 0.8703 (ttpp) cc_final: 0.8157 (tttp) REVERT: P 54 TYR cc_start: 0.7763 (m-80) cc_final: 0.7541 (m-80) REVERT: P 109 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7882 (tt) REVERT: P 113 HIS cc_start: 0.8995 (t70) cc_final: 0.8773 (t-90) REVERT: P 125 GLN cc_start: 0.8465 (mt0) cc_final: 0.8261 (mt0) REVERT: Q 27 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8159 (mm-40) REVERT: Q 30 THR cc_start: 0.9367 (p) cc_final: 0.8830 (t) REVERT: Q 67 ARG cc_start: 0.8378 (ttm110) cc_final: 0.8133 (ttp-110) REVERT: Q 74 GLU cc_start: 0.8311 (tt0) cc_final: 0.8038 (tt0) REVERT: Q 84 MET cc_start: 0.8062 (mmt) cc_final: 0.7705 (mmt) REVERT: n 35 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7390 (mtm-85) REVERT: n 73 ASN cc_start: 0.8749 (t0) cc_final: 0.8374 (t0) REVERT: n 74 LYS cc_start: 0.9038 (mttt) cc_final: 0.8531 (tttt) REVERT: p 76 GLN cc_start: 0.8643 (pt0) cc_final: 0.7804 (tp40) outliers start: 35 outliers final: 22 residues processed: 298 average time/residue: 0.1350 time to fit residues: 56.7964 Evaluate side-chains 301 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 74 GLN 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 24 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 84 GLN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 52 THR 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 49 VAL Chi-restraints excluded: chain n residue 79 ILE 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 92 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 100 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.212488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.135142 restraints weight = 21445.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139948 restraints weight = 11273.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142920 restraints weight = 7870.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.144608 restraints weight = 6517.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.145502 restraints weight = 5924.825| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15174 Z= 0.154 Angle : 0.855 37.158 21681 Z= 0.384 Chirality : 0.041 0.192 2459 Planarity : 0.004 0.063 1791 Dihedral : 28.487 151.760 4242 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 3.33 % Allowed : 18.39 % Favored : 78.28 % 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: 1.67 (0.25), residues: 1073 helix: 2.00 (0.19), residues: 683 sheet: 1.82 (1.37), residues: 18 loop : -0.62 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG n 35 TYR 0.015 0.002 TYR O 42 PHE 0.018 0.002 PHE A 46 TRP 0.010 0.001 TRP B 34 HIS 0.012 0.001 HIS n 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (15158) covalent geometry : angle 0.65514 / 0.37 (21663) hydrogen bonds : bond 0.05267 / 3.51 ( 892) hydrogen bonds : angle 3.72498 / 2.72 ( 2280) metal coordination : bond 0.01085 / 0.65 ( 16) metal coordination : angle 19.09395 / 13.54 ( 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 306 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8062 (mtm-85) REVERT: A 81 GLN cc_start: 0.9266 (pm20) cc_final: 0.8851 (pm20) REVERT: A 347 MET cc_start: 0.4303 (tpp) cc_final: 0.3961 (tpp) REVERT: N 36 LYS cc_start: 0.8427 (tttt) cc_final: 0.8108 (tttt) REVERT: N 74 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8559 (mmmm) REVERT: N 95 LYS cc_start: 0.8968 (tppp) cc_final: 0.8117 (tptp) REVERT: O 59 MET cc_start: 0.8076 (tpp) cc_final: 0.7585 (tpp) REVERT: O 63 ASN cc_start: 0.8037 (m110) cc_final: 0.7828 (m110) REVERT: O 83 TYR cc_start: 0.7677 (m-10) cc_final: 0.7174 (m-10) REVERT: O 84 ASN cc_start: 0.8693 (t0) cc_final: 0.8131 (t0) REVERT: O 108 LYS cc_start: 0.9010 (mttt) cc_final: 0.8404 (mtpt) REVERT: O 116 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8146 (tttp) REVERT: P 54 TYR cc_start: 0.7758 (m-80) cc_final: 0.7549 (m-80) REVERT: P 109 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7910 (tt) REVERT: Q 27 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8166 (mm-40) REVERT: Q 30 THR cc_start: 0.9375 (p) cc_final: 0.8842 (t) REVERT: Q 74 GLU cc_start: 0.8327 (tt0) cc_final: 0.8078 (tt0) REVERT: Q 84 MET cc_start: 0.8017 (mmt) cc_final: 0.7734 (mmt) REVERT: n 35 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7408 (mtm-85) REVERT: n 73 ASN cc_start: 0.8720 (t0) cc_final: 0.8350 (t0) REVERT: n 74 LYS cc_start: 0.9047 (mttt) cc_final: 0.8552 (tttt) REVERT: p 76 GLN cc_start: 0.8652 (pt0) cc_final: 0.7812 (tp40) outliers start: 31 outliers final: 25 residues processed: 290 average time/residue: 0.1283 time to fit residues: 52.7594 Evaluate side-chains 299 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 B residue 86 CYS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 84 GLN 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 52 THR 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 49 VAL Chi-restraints excluded: chain n residue 79 ILE 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 o residue 90 THR Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 77 LYS Chi-restraints excluded: chain q residue 92 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 51 optimal weight: 0.0670 chunk 1 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 81 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 110 ASN N 112 GLN P 113 HIS P 125 GLN ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 55 GLN ** 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 = 0.4279 r_free = 0.4279 target = 0.206371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127683 restraints weight = 21472.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.132262 restraints weight = 11479.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.135097 restraints weight = 8084.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136583 restraints weight = 6728.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.137530 restraints weight = 6137.637| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 15174 Z= 0.289 Angle : 0.938 41.747 21681 Z= 0.430 Chirality : 0.045 0.233 2459 Planarity : 0.005 0.063 1791 Dihedral : 28.675 154.658 4242 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 3.98 % Allowed : 18.60 % Favored : 77.42 % 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: 1.18 (0.25), residues: 1073 helix: 1.58 (0.19), residues: 683 sheet: 1.88 (1.37), residues: 18 loop : -0.76 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG n 35 TYR 0.025 0.003 TYR n 57 PHE 0.029 0.003 PHE o 70 TRP 0.014 0.002 TRP A 293 HIS 0.012 0.002 HIS n 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.29 (15158) covalent geometry : angle 0.76219 / 0.42 (21663) hydrogen bonds : bond 0.06167 / 4.11 ( 892) hydrogen bonds : angle 4.15218 / 3.02 ( 2280) metal coordination : bond 0.01224 / 0.71 ( 16) metal coordination : angle 18.99786 / 13.65 ( 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 317 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8300 (mtm-85) REVERT: A 347 MET cc_start: 0.4119 (tpp) cc_final: 0.3766 (tpp) REVERT: N 24 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: N 32 ARG cc_start: 0.8708 (ttp80) cc_final: 0.8365 (ttp80) REVERT: N 36 LYS cc_start: 0.8488 (tttt) cc_final: 0.8204 (tttt) REVERT: N 74 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8625 (mmmm) REVERT: O 83 TYR cc_start: 0.7758 (m-10) cc_final: 0.7213 (m-10) REVERT: O 84 ASN cc_start: 0.8687 (t0) cc_final: 0.8179 (t0) REVERT: O 108 LYS cc_start: 0.9079 (mttt) cc_final: 0.8442 (mtpt) REVERT: P 54 TYR cc_start: 0.7851 (m-80) cc_final: 0.7579 (m-80) REVERT: P 93 GLN cc_start: 0.8943 (tt0) cc_final: 0.8718 (tt0) REVERT: P 109 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8111 (tt) REVERT: P 125 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: Q 27 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8442 (mm-40) REVERT: Q 30 THR cc_start: 0.9464 (p) cc_final: 0.8934 (t) REVERT: Q 35 ARG cc_start: 0.8803 (ttm-80) cc_final: 0.8505 (ttm-80) REVERT: Q 84 MET cc_start: 0.8314 (mmt) cc_final: 0.7932 (mmt) REVERT: n 35 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7799 (mtm-85) REVERT: n 73 ASN cc_start: 0.8757 (t0) cc_final: 0.8422 (t0) REVERT: n 74 LYS cc_start: 0.9126 (mttt) cc_final: 0.8625 (tttt) REVERT: p 76 GLN cc_start: 0.8763 (pt0) cc_final: 0.8004 (tp40) REVERT: q 36 ARG cc_start: 0.9127 (mtm-85) cc_final: 0.8556 (mpp80) REVERT: q 88 TYR cc_start: 0.8776 (m-10) cc_final: 0.8258 (m-80) outliers start: 37 outliers final: 28 residues processed: 297 average time/residue: 0.1418 time to fit residues: 58.9430 Evaluate side-chains 306 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 274 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 252 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 43 VAL 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 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 P residue 125 GLN 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 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 62 LEU Chi-restraints excluded: chain q residue 73 THR 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: 0.9990 chunk 82 optimal weight: 50.0000 chunk 78 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 41 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 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 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.210305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.133222 restraints weight = 21266.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138004 restraints weight = 11120.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140968 restraints weight = 7745.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142529 restraints weight = 6403.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.143453 restraints weight = 5834.560| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15174 Z= 0.159 Angle : 0.876 39.498 21681 Z= 0.395 Chirality : 0.042 0.235 2459 Planarity : 0.005 0.061 1791 Dihedral : 28.611 154.230 4242 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.20 % Rotamer: Outliers : 3.44 % Allowed : 19.89 % Favored : 76.67 % 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: 1.51 (0.25), residues: 1073 helix: 1.86 (0.19), residues: 681 sheet: 1.89 (1.38), residues: 18 loop : -0.67 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG Q 92 TYR 0.030 0.002 TYR N 39 PHE 0.015 0.002 PHE O 70 TRP 0.010 0.001 TRP B 34 HIS 0.013 0.002 HIS n 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (15158) covalent geometry : angle 0.68209 / 0.38 (21663) hydrogen bonds : bond 0.05253 / 3.50 ( 892) hydrogen bonds : angle 3.83469 / 2.80 ( 2280) metal coordination : bond 0.01033 / 0.63 ( 16) metal coordination : angle 19.09760 / 13.60 ( 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: 32 poor density : 285 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8914 (mttt) cc_final: 0.8518 (mttt) REVERT: A 71 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8151 (mtm-85) REVERT: A 81 GLN cc_start: 0.9343 (pm20) cc_final: 0.8863 (pm20) REVERT: A 347 MET cc_start: 0.4167 (tpp) cc_final: 0.3836 (tpp) REVERT: N 36 LYS cc_start: 0.8490 (tttt) cc_final: 0.8202 (tttt) REVERT: N 39 TYR cc_start: 0.8357 (m-10) cc_final: 0.8069 (m-10) REVERT: N 74 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8595 (mmmm) REVERT: O 83 TYR cc_start: 0.7678 (m-10) cc_final: 0.7215 (m-10) REVERT: O 84 ASN cc_start: 0.8722 (t0) cc_final: 0.8121 (t0) REVERT: O 108 LYS cc_start: 0.9046 (mttt) cc_final: 0.8440 (mtpt) REVERT: O 116 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8181 (tttp) REVERT: P 109 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7926 (tt) REVERT: P 125 GLN cc_start: 0.8272 (mt0) cc_final: 0.7913 (mt0) REVERT: Q 27 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8417 (mm-40) REVERT: Q 30 THR cc_start: 0.9404 (p) cc_final: 0.8871 (t) REVERT: Q 35 ARG cc_start: 0.8728 (ttm-80) cc_final: 0.8423 (ttm-80) REVERT: Q 84 MET cc_start: 0.8065 (mmt) cc_final: 0.7653 (mmt) REVERT: n 23 LEU cc_start: 0.8823 (mt) cc_final: 0.8622 (mp) REVERT: n 35 ARG cc_start: 0.8094 (ttp-110) cc_final: 0.7771 (mtm-85) REVERT: n 51 MET cc_start: 0.7691 (tmm) cc_final: 0.7378 (tmm) REVERT: n 73 ASN cc_start: 0.8663 (t0) cc_final: 0.8369 (t0) REVERT: n 74 LYS cc_start: 0.9138 (mttt) cc_final: 0.8700 (tttt) REVERT: o 47 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7600 (tt0) REVERT: p 76 GLN cc_start: 0.8712 (pt0) cc_final: 0.7913 (tp40) REVERT: q 36 ARG cc_start: 0.9025 (mtm-85) cc_final: 0.8647 (mpp80) outliers start: 32 outliers final: 24 residues processed: 298 average time/residue: 0.1387 time to fit residues: 58.4653 Evaluate side-chains 306 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 280 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 B residue 86 CYS Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 62 MET Chi-restraints excluded: chain P residue 83 ARG 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 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 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 65 optimal weight: 0.5980 chunk 81 optimal weight: 30.0000 chunk 74 optimal weight: 10.9990 chunk 83 optimal weight: 50.0000 chunk 91 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 10 optimal weight: 40.0000 overall best weight: 2.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN N 24 GLN Q 25 ASN ** n 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 55 GLN ** 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 = 0.4275 r_free = 0.4275 target = 0.205911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127967 restraints weight = 21156.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132560 restraints weight = 11295.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.135380 restraints weight = 7932.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136979 restraints weight = 6583.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.137718 restraints weight = 5994.915| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 15174 Z= 0.287 Angle : 0.945 40.123 21681 Z= 0.432 Chirality : 0.045 0.254 2459 Planarity : 0.005 0.061 1791 Dihedral : 28.713 156.703 4242 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.64 % Rotamer: Outliers : 3.98 % Allowed : 20.54 % Favored : 75.48 % 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: 1.11 (0.25), residues: 1073 helix: 1.50 (0.19), residues: 685 sheet: 1.80 (1.38), residues: 18 loop : -0.75 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG n 35 TYR 0.024 0.002 TYR N 39 PHE 0.029 0.003 PHE o 70 TRP 0.013 0.002 TRP B 34 HIS 0.012 0.002 HIS n 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.29 (15158) covalent geometry : angle 0.77111 / 0.42 (21663) hydrogen bonds : bond 0.05849 / 3.90 ( 892) hydrogen bonds : angle 4.14430 / 3.00 ( 2280) metal coordination : bond 0.01193 / 0.71 ( 16) metal coordination : angle 18.98805 / 13.50 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2659.92 seconds wall clock time: 46 minutes 27.37 seconds (2787.37 seconds total)