Starting phenix.real_space_refine on Wed Mar 4 13:17:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzv_22581/03_2026/7jzv_22581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzv_22581/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7jzv_22581/03_2026/7jzv_22581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzv_22581/03_2026/7jzv_22581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jzv_22581/03_2026/7jzv_22581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzv_22581/03_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-dev-5986/lib/python3.9/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: 3.24, per 1000 atoms: 0.23 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: 1.31 Conformation dependent library (CDL) restraints added in 508.8 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: 2.29 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: 2.82 Time building geometry restraints manager: 1.74 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: 20300 2.42 - 4.84: 1136 4.84 - 7.26: 209 7.26 - 9.68: 17 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: 1723 0.071 - 0.142: 628 0.142 - 0.212: 102 0.212 - 0.283: 4 0.283 - 0.354: 2 Chirality restraints: 2459 Sorted by residual: chirality pdb=" CA CYS B 71 " pdb=" N CYS B 71 " pdb=" C CYS B 71 " pdb=" CB CYS B 71 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA CYS B 53 " pdb=" N CYS B 53 " pdb=" C CYS B 53 " pdb=" CB CYS B 53 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ARG N 88 " pdb=" N ARG N 88 " pdb=" C ARG N 88 " pdb=" CB ARG N 88 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2456 not shown) Planarity restraints: 1791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 347 " 0.024 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C MET A 347 " -0.084 2.00e-02 2.50e+03 pdb=" O MET A 347 " 0.030 2.00e-02 2.50e+03 pdb=" OXT MET A 347 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 102 " -0.024 2.00e-02 2.50e+03 4.85e-02 2.36e+01 pdb=" C GLY Q 102 " 0.084 2.00e-02 2.50e+03 pdb=" O GLY Q 102 " -0.030 2.00e-02 2.50e+03 pdb=" OXT GLY Q 102 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 293 " -0.037 2.00e-02 2.50e+03 1.79e-02 8.05e+00 pdb=" CG TRP A 293 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 293 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 293 " 0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP A 293 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 293 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 293 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 293 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 293 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 293 " -0.020 2.00e-02 2.50e+03 ... (remaining 1788 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 422 2.67 - 3.23: 12480 3.23 - 3.79: 24765 3.79 - 4.34: 34308 4.34 - 4.90: 47805 Nonbonded interactions: 119780 Sorted by model distance: nonbonded pdb=" OG1 THR Q 30 " pdb=" OP2 DA X 58 " model vdw 2.117 3.040 nonbonded pdb=" OP1 DC X 77 " pdb=" OG SER q 47 " model vdw 2.261 3.040 nonbonded pdb=" O ARG A 71 " pdb=" OG SER A 72 " model vdw 2.300 3.040 nonbonded pdb=" OP1 DG Y 67 " pdb=" N VAL p 117 " model vdw 2.306 3.120 nonbonded pdb=" OG SER O 32 " pdb=" OP1 DC X 100 " model vdw 2.334 3.040 ... (remaining 119775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = (chain 'o' and resid 31 through 124) } ncs_group { reference = (chain 'P' and resid 46 through 134) selection = (chain 'p' and resid 46 through 134) } ncs_group { reference = (chain 'Q' and resid 25 through 102) selection = chain 'q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.010 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 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= 0.676 Angle : 1.325 12.099 21681 Z= 0.881 Chirality : 0.069 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 covalent geometry : bond 0.01260 (15158) covalent geometry : angle 1.32456 (21663) hydrogen bonds : bond 0.19128 ( 892) hydrogen bonds : angle 5.82510 ( 2280) metal coordination : bond 0.03260 ( 16) metal coordination : angle 1.84034 ( 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 : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.5569 (tt0) cc_final: 0.5320 (tt0) REVERT: A 25 PRO cc_start: 0.7787 (Cg_exo) cc_final: 0.7279 (Cg_endo) REVERT: A 52 LEU cc_start: 0.7041 (mt) cc_final: 0.5730 (mt) REVERT: N 39 TYR cc_start: 0.8373 (m-80) cc_final: 0.8000 (m-80) REVERT: O 36 SER cc_start: 0.8125 (p) cc_final: 0.7808 (m) REVERT: O 108 LYS cc_start: 0.7870 (mttt) cc_final: 0.7265 (mtpt) REVERT: P 60 LEU cc_start: 0.7035 (mt) cc_final: 0.6811 (mt) REVERT: Q 52 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6911 (mm-30) REVERT: Q 53 GLU cc_start: 0.7836 (tp30) cc_final: 0.7453 (tp30) REVERT: p 60 LEU cc_start: 0.8272 (mt) cc_final: 0.7723 (mt) outliers start: 2 outliers final: 0 residues processed: 329 average time/residue: 0.1560 time to fit residues: 70.1298 Evaluate side-chains 251 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN O 84 ASN P 113 HIS Q 25 ASN ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 76 GLN q 25 ASN q 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.220587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.148693 restraints weight = 21977.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.153831 restraints weight = 11224.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.157054 restraints weight = 7668.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.158766 restraints weight = 6262.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.159864 restraints weight = 5670.161| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15174 Z= 0.189 Angle : 0.858 41.050 21681 Z= 0.396 Chirality : 0.039 0.202 2459 Planarity : 0.005 0.044 1791 Dihedral : 27.660 144.799 4242 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.49 % Favored : 98.42 % Rotamer: Outliers : 2.58 % Allowed : 8.39 % Favored : 89.03 % 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: 1.82 (0.24), residues: 1073 helix: 1.93 (0.19), residues: 686 sheet: 0.32 (1.28), residues: 18 loop : -0.06 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG p 131 TYR 0.027 0.002 TYR B 87 PHE 0.021 0.002 PHE P 67 TRP 0.016 0.002 TRP B 34 HIS 0.009 0.001 HIS q 75 Details of bonding type rmsd covalent geometry : bond 0.00405 (15158) covalent geometry : angle 0.66117 (21663) hydrogen bonds : bond 0.06755 ( 892) hydrogen bonds : angle 3.75033 ( 2280) metal coordination : bond 0.01520 ( 16) metal coordination : angle 19.01313 ( 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 308 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 284 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8700 (mt) cc_final: 0.8134 (mt) REVERT: A 71 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7942 (mtm110) REVERT: A 81 GLN cc_start: 0.9162 (mt0) cc_final: 0.8762 (pt0) REVERT: B 104 MET cc_start: 0.8280 (mmm) cc_final: 0.7868 (mmm) REVERT: N 39 TYR cc_start: 0.9010 (m-80) cc_final: 0.8719 (m-80) REVERT: N 95 LYS cc_start: 0.8920 (tppt) cc_final: 0.7960 (tptt) REVERT: O 36 SER cc_start: 0.8625 (p) cc_final: 0.8378 (m) REVERT: O 99 ARG cc_start: 0.8430 (mtm180) cc_final: 0.7905 (mtm180) REVERT: O 108 LYS cc_start: 0.8744 (mttt) cc_final: 0.8121 (mtpt) REVERT: O 113 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7277 (mm-30) REVERT: O 116 LYS cc_start: 0.8472 (ttpp) cc_final: 0.8075 (ptmm) REVERT: P 73 GLU cc_start: 0.7617 (tp30) cc_final: 0.7355 (tp30) REVERT: P 93 GLN cc_start: 0.8835 (tt0) cc_final: 0.8515 (tt0) REVERT: Q 35 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.7570 (mtp85) REVERT: Q 44 LYS cc_start: 0.8894 (tttm) cc_final: 0.8634 (tttm) REVERT: Q 52 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7836 (mm-30) REVERT: Q 74 GLU cc_start: 0.8235 (tt0) cc_final: 0.7765 (tt0) REVERT: n 51 MET cc_start: 0.7425 (ttt) cc_final: 0.7191 (ttt) REVERT: n 84 GLN cc_start: 0.8082 (tt0) cc_final: 0.7748 (tt0) REVERT: n 88 ARG cc_start: 0.7647 (mmt180) cc_final: 0.7241 (tpp80) REVERT: n 95 LYS cc_start: 0.8759 (mttt) cc_final: 0.8049 (ttmt) REVERT: p 120 MET cc_start: 0.7789 (mmm) cc_final: 0.7545 (mmm) outliers start: 24 outliers final: 15 residues processed: 295 average time/residue: 0.1392 time to fit residues: 57.7447 Evaluate side-chains 276 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 A residue 338 SER Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 57 SER 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 p residue 86 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN N 24 GLN N 94 ASN N 110 ASN N 112 GLN P 93 GLN P 113 HIS ** o 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 93 GLN q 25 ASN q 27 GLN ** q 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 93 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.208764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.132016 restraints weight = 21799.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.136786 restraints weight = 11442.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.139659 restraints weight = 7928.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141394 restraints weight = 6546.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.142220 restraints weight = 5928.770| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 15174 Z= 0.282 Angle : 0.787 23.403 21681 Z= 0.405 Chirality : 0.042 0.290 2459 Planarity : 0.005 0.047 1791 Dihedral : 28.291 146.231 4242 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 3.33 % Allowed : 11.72 % Favored : 84.95 % 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: 1.29 (0.24), residues: 1073 helix: 1.56 (0.19), residues: 689 sheet: 1.15 (1.30), residues: 18 loop : -0.46 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG n 35 TYR 0.022 0.002 TYR n 57 PHE 0.025 0.003 PHE P 67 TRP 0.012 0.002 TRP B 34 HIS 0.009 0.002 HIS p 113 Details of bonding type rmsd covalent geometry : bond 0.00634 (15158) covalent geometry : angle 0.70527 (21663) hydrogen bonds : bond 0.05765 ( 892) hydrogen bonds : angle 3.89218 ( 2280) metal coordination : bond 0.02166 ( 16) metal coordination : angle 12.12374 ( 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 341 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 310 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8893 (mt) cc_final: 0.8659 (mt) REVERT: A 71 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8231 (mtm-85) REVERT: A 81 GLN cc_start: 0.9315 (mt0) cc_final: 0.9096 (pt0) REVERT: N 20 ARG cc_start: 0.8676 (mtt90) cc_final: 0.8207 (mtt-85) REVERT: N 36 LYS cc_start: 0.8333 (tttt) cc_final: 0.8084 (tttt) REVERT: N 42 ARG cc_start: 0.8949 (mtp180) cc_final: 0.8744 (mtp180) REVERT: N 74 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8588 (mmmm) REVERT: N 94 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8476 (t0) REVERT: N 95 LYS cc_start: 0.9045 (tppt) cc_final: 0.8774 (tppp) REVERT: O 59 MET cc_start: 0.8864 (tpp) cc_final: 0.8326 (tpp) REVERT: O 84 ASN cc_start: 0.8644 (t0) cc_final: 0.8398 (t0) REVERT: O 85 LYS cc_start: 0.8463 (tppt) cc_final: 0.8254 (ttmt) REVERT: O 108 LYS cc_start: 0.9070 (mttt) cc_final: 0.8473 (mtpt) REVERT: O 116 LYS cc_start: 0.8704 (ttpp) cc_final: 0.8134 (tttp) REVERT: P 54 TYR cc_start: 0.7851 (m-80) cc_final: 0.7640 (m-80) REVERT: P 100 LEU cc_start: 0.9413 (mt) cc_final: 0.9183 (mt) REVERT: P 125 GLN cc_start: 0.8390 (mt0) cc_final: 0.8040 (mt0) REVERT: Q 27 GLN cc_start: 0.8854 (mm110) cc_final: 0.8515 (mm-40) REVERT: Q 30 THR cc_start: 0.9456 (p) cc_final: 0.8955 (t) REVERT: Q 74 GLU cc_start: 0.8265 (tt0) cc_final: 0.8010 (tt0) REVERT: n 51 MET cc_start: 0.7754 (ttt) cc_final: 0.7550 (ttt) REVERT: n 74 LYS cc_start: 0.8967 (mttt) cc_final: 0.8479 (tttt) REVERT: n 84 GLN cc_start: 0.8101 (tt0) cc_final: 0.7876 (tt0) REVERT: o 71 GLU cc_start: 0.7365 (tp30) cc_final: 0.7115 (tp30) REVERT: o 99 ARG cc_start: 0.8746 (mtp180) cc_final: 0.8491 (mmm-85) REVERT: q 79 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8686 (mttp) REVERT: q 88 TYR cc_start: 0.8788 (m-10) cc_final: 0.8201 (m-80) outliers start: 31 outliers final: 18 residues processed: 321 average time/residue: 0.1409 time to fit residues: 63.2795 Evaluate side-chains 305 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 285 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 N residue 43 VAL Chi-restraints excluded: chain N residue 94 ASN Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 83 ARG 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 66 VAL Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 112 ILE 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: 3.9990 chunk 15 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 14 optimal weight: 8.9990 chunk 55 optimal weight: 0.0030 chunk 66 optimal weight: 0.8980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN N 24 GLN O 63 ASN O 82 HIS q 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.213560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136995 restraints weight = 21688.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.141914 restraints weight = 11259.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.145024 restraints weight = 7783.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.146777 restraints weight = 6408.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.147702 restraints weight = 5805.640| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15174 Z= 0.154 Angle : 0.690 24.301 21681 Z= 0.346 Chirality : 0.036 0.192 2459 Planarity : 0.004 0.058 1791 Dihedral : 27.977 148.964 4242 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.58 % Favored : 98.32 % Rotamer: Outliers : 2.58 % Allowed : 15.81 % Favored : 81.61 % 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: 1.79 (0.25), residues: 1073 helix: 2.03 (0.19), residues: 687 sheet: 1.34 (1.32), residues: 18 loop : -0.43 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 79 TYR 0.020 0.002 TYR o 40 PHE 0.015 0.002 PHE P 78 TRP 0.009 0.001 TRP B 34 HIS 0.013 0.002 HIS n 31 Details of bonding type rmsd covalent geometry : bond 0.00332 (15158) covalent geometry : angle 0.59764 (21663) hydrogen bonds : bond 0.04681 ( 892) hydrogen bonds : angle 3.43377 ( 2280) metal coordination : bond 0.01142 ( 16) metal coordination : angle 12.00427 ( 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 311 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8798 (mttt) cc_final: 0.8492 (mttt) REVERT: A 71 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8069 (mtm-85) REVERT: A 81 GLN cc_start: 0.9255 (mt0) cc_final: 0.9039 (pt0) REVERT: N 24 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7731 (mp10) REVERT: N 36 LYS cc_start: 0.8315 (tttt) cc_final: 0.8027 (tttt) REVERT: N 39 TYR cc_start: 0.8765 (m-80) cc_final: 0.8249 (m-10) REVERT: N 56 GLU cc_start: 0.7802 (tt0) cc_final: 0.7428 (tt0) REVERT: N 74 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8584 (mmmm) REVERT: N 95 LYS cc_start: 0.9026 (tppt) cc_final: 0.8067 (tptt) REVERT: O 59 MET cc_start: 0.8496 (tpp) cc_final: 0.7896 (mmm) REVERT: O 63 ASN cc_start: 0.8102 (m110) cc_final: 0.7715 (m110) REVERT: O 84 ASN cc_start: 0.8654 (t0) cc_final: 0.8359 (t0) REVERT: O 85 LYS cc_start: 0.8411 (tppt) cc_final: 0.8201 (ttmt) REVERT: O 108 LYS cc_start: 0.8952 (mttt) cc_final: 0.8368 (mtpt) REVERT: O 116 LYS cc_start: 0.8717 (ttpp) cc_final: 0.8143 (tttp) REVERT: P 73 GLU cc_start: 0.8054 (tp30) cc_final: 0.7843 (tp30) REVERT: P 125 GLN cc_start: 0.8475 (mt0) cc_final: 0.8139 (mt0) REVERT: Q 27 GLN cc_start: 0.8809 (mm110) cc_final: 0.8212 (mm110) REVERT: Q 44 LYS cc_start: 0.8811 (tttm) cc_final: 0.8239 (ttmm) REVERT: Q 74 GLU cc_start: 0.8242 (tt0) cc_final: 0.7929 (tt0) REVERT: Q 84 MET cc_start: 0.7935 (mmt) cc_final: 0.7580 (mmt) REVERT: n 74 LYS cc_start: 0.9049 (mttt) cc_final: 0.8570 (tttt) REVERT: n 84 GLN cc_start: 0.8007 (tt0) cc_final: 0.7678 (tt0) REVERT: o 47 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7610 (tt0) REVERT: o 93 GLU cc_start: 0.8301 (mp0) cc_final: 0.8068 (mp0) REVERT: o 99 ARG cc_start: 0.8704 (mtp180) cc_final: 0.8273 (ttm170) outliers start: 24 outliers final: 16 residues processed: 295 average time/residue: 0.1406 time to fit residues: 58.3826 Evaluate side-chains 289 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 271 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 289 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 54 ILE 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 87 SER Chi-restraints excluded: chain p residue 97 GLU Chi-restraints excluded: chain q residue 62 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 121 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 94 ASN O 63 ASN P 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.210818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.133619 restraints weight = 21587.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.138475 restraints weight = 11329.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141426 restraints weight = 7875.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.143121 restraints weight = 6504.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.143906 restraints weight = 5917.202| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15174 Z= 0.185 Angle : 0.699 23.832 21681 Z= 0.350 Chirality : 0.037 0.224 2459 Planarity : 0.004 0.059 1791 Dihedral : 27.930 151.472 4242 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 3.98 % Allowed : 15.05 % 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: 1.76 (0.25), residues: 1073 helix: 2.04 (0.19), residues: 684 sheet: 1.47 (1.33), residues: 18 loop : -0.50 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 79 TYR 0.028 0.002 TYR o 40 PHE 0.016 0.002 PHE P 78 TRP 0.010 0.001 TRP B 34 HIS 0.014 0.002 HIS n 31 Details of bonding type rmsd covalent geometry : bond 0.00411 (15158) covalent geometry : angle 0.61495 (21663) hydrogen bonds : bond 0.04678 ( 892) hydrogen bonds : angle 3.54946 ( 2280) metal coordination : bond 0.01033 ( 16) metal coordination : angle 11.53560 ( 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 312 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 275 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8888 (mttt) cc_final: 0.8557 (mttt) REVERT: A 71 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8115 (mtm-85) REVERT: N 36 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8102 (tttt) REVERT: N 39 TYR cc_start: 0.8652 (m-80) cc_final: 0.8262 (m-10) REVERT: N 74 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8601 (mmmm) REVERT: N 94 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8387 (t0) REVERT: O 37 TYR cc_start: 0.8716 (m-80) cc_final: 0.8497 (m-80) REVERT: O 59 MET cc_start: 0.8633 (tpp) cc_final: 0.8161 (tpp) REVERT: O 63 ASN cc_start: 0.8236 (m-40) cc_final: 0.7995 (m-40) REVERT: O 71 GLU cc_start: 0.8390 (tp30) cc_final: 0.8013 (tp30) REVERT: O 84 ASN cc_start: 0.8720 (t0) cc_final: 0.8385 (t0) REVERT: O 85 LYS cc_start: 0.8472 (tppt) cc_final: 0.8235 (ttmt) REVERT: O 108 LYS cc_start: 0.9000 (mttt) cc_final: 0.8423 (mtpt) REVERT: O 116 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8206 (tttp) REVERT: P 125 GLN cc_start: 0.8362 (mt0) cc_final: 0.8058 (mt0) REVERT: Q 27 GLN cc_start: 0.8803 (mm110) cc_final: 0.8316 (mm110) REVERT: Q 30 THR cc_start: 0.9367 (p) cc_final: 0.8844 (t) REVERT: Q 44 LYS cc_start: 0.8815 (tttm) cc_final: 0.8241 (ttmm) REVERT: Q 59 LYS cc_start: 0.8442 (tttm) cc_final: 0.8160 (tptm) REVERT: Q 74 GLU cc_start: 0.8253 (tt0) cc_final: 0.7948 (tt0) REVERT: n 35 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7515 (mtm-85) REVERT: n 73 ASN cc_start: 0.8712 (t0) cc_final: 0.8045 (t0) REVERT: n 74 LYS cc_start: 0.9103 (mttt) cc_final: 0.8574 (tttt) REVERT: o 99 ARG cc_start: 0.8748 (mtp180) cc_final: 0.8356 (ttm170) outliers start: 37 outliers final: 25 residues processed: 289 average time/residue: 0.1383 time to fit residues: 55.9709 Evaluate side-chains 300 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 320 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 36 LYS Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 94 ASN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 42 TYR Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 86 SER 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 101 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 71 THR Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 73 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 94 ASN ** 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 = 0.4320 r_free = 0.4320 target = 0.210378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133486 restraints weight = 21492.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.138334 restraints weight = 11287.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141268 restraints weight = 7836.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142938 restraints weight = 6484.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143741 restraints weight = 5889.080| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15174 Z= 0.186 Angle : 0.700 23.630 21681 Z= 0.349 Chirality : 0.036 0.211 2459 Planarity : 0.004 0.057 1791 Dihedral : 27.899 153.199 4242 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.58 % Rotamer: Outliers : 3.55 % Allowed : 17.53 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.25), residues: 1073 helix: 2.07 (0.19), residues: 684 sheet: 1.62 (1.38), residues: 18 loop : -0.53 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 79 TYR 0.028 0.002 TYR o 40 PHE 0.016 0.002 PHE P 78 TRP 0.010 0.001 TRP B 34 HIS 0.010 0.001 HIS n 31 Details of bonding type rmsd covalent geometry : bond 0.00415 (15158) covalent geometry : angle 0.61367 (21663) hydrogen bonds : bond 0.04537 ( 892) hydrogen bonds : angle 3.54572 ( 2280) metal coordination : bond 0.01014 ( 16) metal coordination : angle 11.72775 ( 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 306 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 273 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8882 (mttt) cc_final: 0.8549 (mttt) REVERT: A 78 ARG cc_start: 0.8976 (mmp80) cc_final: 0.8701 (mmm-85) REVERT: N 36 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7992 (tttt) REVERT: N 39 TYR cc_start: 0.8663 (m-80) cc_final: 0.8266 (m-10) REVERT: N 74 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8647 (mmmm) REVERT: N 95 LYS cc_start: 0.8958 (tppp) cc_final: 0.8131 (tptt) REVERT: O 37 TYR cc_start: 0.8780 (m-80) cc_final: 0.8556 (m-80) REVERT: O 63 ASN cc_start: 0.8286 (m-40) cc_final: 0.8005 (m-40) REVERT: O 71 GLU cc_start: 0.8350 (tp30) cc_final: 0.7951 (tp30) REVERT: O 84 ASN cc_start: 0.8737 (t0) cc_final: 0.8375 (t0) REVERT: O 108 LYS cc_start: 0.8989 (mttt) cc_final: 0.8430 (mtpt) REVERT: O 116 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8203 (tttp) REVERT: P 125 GLN cc_start: 0.8384 (mt0) cc_final: 0.8080 (mt0) REVERT: Q 27 GLN cc_start: 0.8801 (mm110) cc_final: 0.8349 (mm-40) REVERT: Q 30 THR cc_start: 0.9378 (p) cc_final: 0.8871 (t) REVERT: Q 44 LYS cc_start: 0.8816 (tttm) cc_final: 0.8221 (ttmm) REVERT: Q 59 LYS cc_start: 0.8474 (tttm) cc_final: 0.8162 (tptm) REVERT: n 73 ASN cc_start: 0.8722 (t0) cc_final: 0.8067 (t0) REVERT: n 74 LYS cc_start: 0.9142 (mttt) cc_final: 0.8498 (tptm) REVERT: o 47 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7653 (tt0) REVERT: o 71 GLU cc_start: 0.7558 (tp30) cc_final: 0.7128 (tp30) REVERT: o 99 ARG cc_start: 0.8709 (mtp180) cc_final: 0.8324 (ttm170) outliers start: 33 outliers final: 24 residues processed: 285 average time/residue: 0.1463 time to fit residues: 58.3958 Evaluate side-chains 296 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 271 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 320 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LYS Chi-restraints excluded: chain N residue 43 VAL 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 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 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 101 THR Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 71 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: 0.5980 chunk 85 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 127 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 94 ASN ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 31 HIS ** p 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.210601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137551 restraints weight = 20917.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142229 restraints weight = 10644.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.145161 restraints weight = 7296.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.146821 restraints weight = 5981.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.147591 restraints weight = 5409.868| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15174 Z= 0.154 Angle : 0.685 24.165 21681 Z= 0.339 Chirality : 0.035 0.212 2459 Planarity : 0.004 0.057 1791 Dihedral : 27.832 154.529 4242 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.77 % Favored : 98.14 % Rotamer: Outliers : 2.47 % Allowed : 19.03 % Favored : 78.49 % 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: 1.97 (0.25), residues: 1073 helix: 2.22 (0.19), residues: 685 sheet: 1.55 (1.37), residues: 18 loop : -0.46 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG n 35 TYR 0.032 0.002 TYR o 40 PHE 0.014 0.002 PHE P 67 TRP 0.009 0.001 TRP B 34 HIS 0.008 0.001 HIS p 113 Details of bonding type rmsd covalent geometry : bond 0.00334 (15158) covalent geometry : angle 0.59843 (21663) hydrogen bonds : bond 0.04270 ( 892) hydrogen bonds : angle 3.44621 ( 2280) metal coordination : bond 0.00888 ( 16) metal coordination : angle 11.59735 ( 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 308 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 285 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.8401 (Cg_exo) cc_final: 0.8182 (Cg_endo) REVERT: A 45 LYS cc_start: 0.8895 (mttt) cc_final: 0.8569 (mttt) REVERT: A 78 ARG cc_start: 0.8931 (mmp80) cc_final: 0.8624 (mmm-85) REVERT: N 20 ARG cc_start: 0.8599 (mtt90) cc_final: 0.8322 (mtm-85) REVERT: N 36 LYS cc_start: 0.8363 (tttt) cc_final: 0.7998 (tttt) REVERT: N 39 TYR cc_start: 0.8664 (m-80) cc_final: 0.8237 (m-10) REVERT: N 74 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8649 (mmmm) REVERT: O 37 TYR cc_start: 0.8799 (m-80) cc_final: 0.8571 (m-80) REVERT: O 59 MET cc_start: 0.8712 (tpp) cc_final: 0.8178 (tpp) REVERT: O 63 ASN cc_start: 0.8294 (m-40) cc_final: 0.7994 (m-40) REVERT: O 71 GLU cc_start: 0.8433 (tp30) cc_final: 0.7986 (tp30) REVERT: O 84 ASN cc_start: 0.8759 (t0) cc_final: 0.8365 (t0) REVERT: O 108 LYS cc_start: 0.8911 (mttt) cc_final: 0.8344 (mtpt) REVERT: O 116 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8155 (tttp) REVERT: P 125 GLN cc_start: 0.8402 (mt0) cc_final: 0.8080 (mt0) REVERT: Q 27 GLN cc_start: 0.8810 (mm110) cc_final: 0.8323 (mm-40) REVERT: Q 59 LYS cc_start: 0.8388 (tttm) cc_final: 0.8126 (tptm) REVERT: Q 67 ARG cc_start: 0.8249 (ttm110) cc_final: 0.8015 (ttp-110) REVERT: n 73 ASN cc_start: 0.8708 (t0) cc_final: 0.8153 (t0) REVERT: n 74 LYS cc_start: 0.9132 (mttt) cc_final: 0.8564 (tptm) REVERT: o 47 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7738 (tt0) REVERT: o 71 GLU cc_start: 0.7539 (tp30) cc_final: 0.7214 (tp30) REVERT: o 99 ARG cc_start: 0.8653 (mtp180) cc_final: 0.8276 (ttm170) outliers start: 23 outliers final: 20 residues processed: 293 average time/residue: 0.1445 time to fit residues: 58.8486 Evaluate side-chains 297 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 277 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain N residue 43 VAL 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 N residue 102 ILE Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain O residue 49 HIS Chi-restraints excluded: chain P residue 83 ARG 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 n residue 101 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 62 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 100 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 94 ASN ** Q 25 ASN ** 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 = 0.4330 r_free = 0.4330 target = 0.211577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.134922 restraints weight = 21403.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.139758 restraints weight = 11208.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.142711 restraints weight = 7797.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.144362 restraints weight = 6456.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.145175 restraints weight = 5878.724| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15174 Z= 0.162 Angle : 0.687 24.023 21681 Z= 0.338 Chirality : 0.035 0.170 2459 Planarity : 0.004 0.070 1791 Dihedral : 27.789 156.213 4242 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 3.12 % Allowed : 18.60 % 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: 2.02 (0.25), residues: 1073 helix: 2.23 (0.19), residues: 687 sheet: 1.61 (1.37), residues: 18 loop : -0.40 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 79 TYR 0.030 0.002 TYR o 40 PHE 0.025 0.002 PHE o 70 TRP 0.010 0.001 TRP B 34 HIS 0.008 0.001 HIS n 31 Details of bonding type rmsd covalent geometry : bond 0.00356 (15158) covalent geometry : angle 0.60103 (21663) hydrogen bonds : bond 0.04222 ( 892) hydrogen bonds : angle 3.43177 ( 2280) metal coordination : bond 0.00814 ( 16) metal coordination : angle 11.57495 ( 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 317 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 288 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.8483 (Cg_exo) cc_final: 0.8270 (Cg_endo) REVERT: A 45 LYS cc_start: 0.8909 (mttt) cc_final: 0.8572 (mttt) REVERT: A 78 ARG cc_start: 0.8873 (mmp80) cc_final: 0.8666 (mmp80) REVERT: A 81 GLN cc_start: 0.9187 (mt0) cc_final: 0.8825 (tm-30) REVERT: N 20 ARG cc_start: 0.8610 (mtt90) cc_final: 0.8388 (mtm-85) REVERT: N 36 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7952 (tttt) REVERT: N 39 TYR cc_start: 0.8624 (m-80) cc_final: 0.8223 (m-10) REVERT: N 61 GLU cc_start: 0.8387 (tp30) cc_final: 0.8045 (tp30) REVERT: N 74 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8619 (mmmm) REVERT: O 37 TYR cc_start: 0.8804 (m-80) cc_final: 0.8576 (m-80) REVERT: O 59 MET cc_start: 0.8709 (tpp) cc_final: 0.8019 (mmm) REVERT: O 63 ASN cc_start: 0.8280 (m-40) cc_final: 0.7879 (m-40) REVERT: O 71 GLU cc_start: 0.8340 (tp30) cc_final: 0.7859 (tp30) REVERT: O 84 ASN cc_start: 0.8727 (t0) cc_final: 0.8403 (t0) REVERT: O 108 LYS cc_start: 0.8906 (mttt) cc_final: 0.8330 (mtpt) REVERT: O 116 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8138 (tttp) REVERT: P 125 GLN cc_start: 0.8383 (mt0) cc_final: 0.8077 (mt0) REVERT: Q 27 GLN cc_start: 0.8859 (mm110) cc_final: 0.8398 (mm-40) REVERT: Q 59 LYS cc_start: 0.8437 (tttm) cc_final: 0.8166 (tptm) REVERT: n 73 ASN cc_start: 0.8745 (t0) cc_final: 0.8201 (t0) REVERT: n 74 LYS cc_start: 0.9171 (mttt) cc_final: 0.8641 (tptm) REVERT: o 47 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7682 (tt0) REVERT: o 71 GLU cc_start: 0.7578 (tp30) cc_final: 0.7326 (tp30) REVERT: o 99 ARG cc_start: 0.8672 (mtp180) cc_final: 0.8302 (ttm170) outliers start: 29 outliers final: 25 residues processed: 297 average time/residue: 0.1409 time to fit residues: 58.4669 Evaluate side-chains 309 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain N residue 36 LYS Chi-restraints excluded: chain N residue 43 VAL 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 N residue 102 ILE Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain P residue 83 ARG 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 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 87 SER Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 77 LYS Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 12 optimal weight: 0.0040 chunk 51 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 94 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 94 ASN ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 HIS n 38 ASN ** 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 = 0.4347 r_free = 0.4347 target = 0.213235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137324 restraints weight = 21593.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.142246 restraints weight = 11180.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.145242 restraints weight = 7736.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.146957 restraints weight = 6384.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.147746 restraints weight = 5800.342| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15174 Z= 0.146 Angle : 0.693 24.018 21681 Z= 0.340 Chirality : 0.036 0.224 2459 Planarity : 0.004 0.053 1791 Dihedral : 27.744 156.721 4242 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.05 % Favored : 97.86 % Rotamer: Outliers : 2.69 % Allowed : 20.22 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.25), residues: 1073 helix: 2.28 (0.19), residues: 685 sheet: 1.75 (1.37), residues: 18 loop : -0.43 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 79 TYR 0.028 0.001 TYR o 40 PHE 0.019 0.002 PHE o 70 TRP 0.015 0.001 TRP B 34 HIS 0.020 0.001 HIS n 31 Details of bonding type rmsd covalent geometry : bond 0.00314 (15158) covalent geometry : angle 0.61247 (21663) hydrogen bonds : bond 0.04119 ( 892) hydrogen bonds : angle 3.40192 ( 2280) metal coordination : bond 0.00807 ( 16) metal coordination : angle 11.29974 ( 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 307 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 282 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.8475 (Cg_exo) cc_final: 0.8265 (Cg_endo) REVERT: A 45 LYS cc_start: 0.8922 (mttt) cc_final: 0.8582 (mttt) REVERT: A 81 GLN cc_start: 0.9254 (mt0) cc_final: 0.8884 (tm-30) REVERT: B 43 ARG cc_start: 0.8709 (ptp-110) cc_final: 0.8393 (ptp90) REVERT: N 20 ARG cc_start: 0.8582 (mtt90) cc_final: 0.8295 (mtm-85) REVERT: N 36 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7931 (tttt) REVERT: N 39 TYR cc_start: 0.8591 (m-80) cc_final: 0.8203 (m-10) REVERT: N 61 GLU cc_start: 0.8339 (tp30) cc_final: 0.7924 (tt0) REVERT: N 74 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8631 (mmmm) REVERT: N 95 LYS cc_start: 0.8985 (tppp) cc_final: 0.8090 (tptt) REVERT: O 37 TYR cc_start: 0.8767 (m-80) cc_final: 0.8508 (m-80) REVERT: O 59 MET cc_start: 0.8668 (tpp) cc_final: 0.8406 (mmm) REVERT: O 71 GLU cc_start: 0.8393 (tp30) cc_final: 0.7848 (tp30) REVERT: O 84 ASN cc_start: 0.8727 (t0) cc_final: 0.8388 (t0) REVERT: O 108 LYS cc_start: 0.8908 (mttt) cc_final: 0.8312 (mtpt) REVERT: O 116 LYS cc_start: 0.8702 (ttpp) cc_final: 0.8156 (tttp) REVERT: P 125 GLN cc_start: 0.8400 (mt0) cc_final: 0.8038 (mt0) REVERT: Q 27 GLN cc_start: 0.8858 (mm110) cc_final: 0.8384 (mm-40) REVERT: Q 59 LYS cc_start: 0.8342 (tttm) cc_final: 0.8101 (tptm) REVERT: Q 67 ARG cc_start: 0.8293 (ttm110) cc_final: 0.7974 (ttp-110) REVERT: n 73 ASN cc_start: 0.8735 (t0) cc_final: 0.8203 (t0) REVERT: n 74 LYS cc_start: 0.9189 (mttt) cc_final: 0.8657 (tptm) REVERT: o 47 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7587 (tt0) REVERT: o 71 GLU cc_start: 0.7555 (tp30) cc_final: 0.7310 (tp30) REVERT: o 99 ARG cc_start: 0.8641 (mtp180) cc_final: 0.8300 (ttm170) outliers start: 25 outliers final: 20 residues processed: 290 average time/residue: 0.1458 time to fit residues: 58.2587 Evaluate side-chains 293 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 272 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain N residue 36 LYS Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 94 ASN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain P residue 83 ARG 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 58 LEU Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 87 SER Chi-restraints excluded: chain o residue 122 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 94 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.0000 chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 38 ASN ** 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 = 0.4285 r_free = 0.4285 target = 0.206922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.128980 restraints weight = 21240.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133513 restraints weight = 11340.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136413 restraints weight = 7989.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137992 restraints weight = 6657.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138727 restraints weight = 6069.074| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 15174 Z= 0.270 Angle : 0.763 21.794 21681 Z= 0.381 Chirality : 0.039 0.193 2459 Planarity : 0.005 0.078 1791 Dihedral : 27.903 159.347 4242 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 3.01 % Allowed : 20.00 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.25), residues: 1073 helix: 1.88 (0.19), residues: 677 sheet: 1.88 (1.39), residues: 18 loop : -0.63 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 79 TYR 0.032 0.002 TYR o 40 PHE 0.028 0.002 PHE o 70 TRP 0.013 0.002 TRP B 34 HIS 0.016 0.002 HIS n 31 Details of bonding type rmsd covalent geometry : bond 0.00621 (15158) covalent geometry : angle 0.68901 (21663) hydrogen bonds : bond 0.04990 ( 892) hydrogen bonds : angle 3.82367 ( 2280) metal coordination : bond 0.00993 ( 16) metal coordination : angle 11.40207 ( 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: 28 poor density : 289 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8924 (mttt) cc_final: 0.8587 (mttt) REVERT: A 51 LEU cc_start: 0.7844 (tt) cc_final: 0.7633 (tt) REVERT: B 43 ARG cc_start: 0.8657 (ptp-110) cc_final: 0.8454 (ptp-170) REVERT: N 20 ARG cc_start: 0.8596 (mtt90) cc_final: 0.8206 (mtm-85) REVERT: N 36 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8101 (tttt) REVERT: N 39 TYR cc_start: 0.8629 (m-80) cc_final: 0.8090 (m-10) REVERT: N 61 GLU cc_start: 0.8399 (tp30) cc_final: 0.8022 (tt0) REVERT: N 74 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8647 (mmmm) REVERT: N 95 LYS cc_start: 0.8915 (tppp) cc_final: 0.8032 (tptt) REVERT: O 47 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7908 (tt0) REVERT: O 83 TYR cc_start: 0.7742 (m-10) cc_final: 0.7037 (m-10) REVERT: O 84 ASN cc_start: 0.8790 (t0) cc_final: 0.8451 (t0) REVERT: O 108 LYS cc_start: 0.9018 (mttt) cc_final: 0.8465 (mtpt) REVERT: O 116 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8076 (mtmm) REVERT: P 125 GLN cc_start: 0.8426 (mt0) cc_final: 0.8114 (mt0) REVERT: Q 27 GLN cc_start: 0.8923 (mm110) cc_final: 0.8488 (mm-40) REVERT: Q 30 THR cc_start: 0.9438 (p) cc_final: 0.8941 (t) REVERT: n 35 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7309 (mtm-85) REVERT: n 73 ASN cc_start: 0.8722 (t0) cc_final: 0.8195 (t0) REVERT: n 74 LYS cc_start: 0.9184 (mttt) cc_final: 0.8722 (tttt) REVERT: o 71 GLU cc_start: 0.7548 (tp30) cc_final: 0.7248 (tp30) REVERT: p 116 ARG cc_start: 0.8638 (ptp90) cc_final: 0.6465 (ptp90) outliers start: 28 outliers final: 20 residues processed: 297 average time/residue: 0.1528 time to fit residues: 62.1996 Evaluate side-chains 304 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain N residue 36 LYS Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 124 ILE 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 87 SER Chi-restraints excluded: chain o residue 122 THR Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 65 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 40 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 chunk 116 optimal weight: 0.1980 chunk 10 optimal weight: 40.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 94 ASN ** P 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 38 ASN ** p 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.209565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.133043 restraints weight = 21286.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.137802 restraints weight = 11158.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140768 restraints weight = 7768.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142451 restraints weight = 6421.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.143347 restraints weight = 5836.575| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15174 Z= 0.184 Angle : 0.714 22.248 21681 Z= 0.354 Chirality : 0.036 0.163 2459 Planarity : 0.005 0.063 1791 Dihedral : 27.910 160.950 4242 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.52 % Favored : 97.39 % Rotamer: Outliers : 2.58 % Allowed : 21.29 % Favored : 76.13 % 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: 1.71 (0.25), residues: 1073 helix: 2.02 (0.19), residues: 682 sheet: 1.84 (1.38), residues: 18 loop : -0.57 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG q 95 TYR 0.031 0.002 TYR o 40 PHE 0.022 0.002 PHE o 70 TRP 0.012 0.001 TRP B 34 HIS 0.016 0.001 HIS n 31 Details of bonding type rmsd covalent geometry : bond 0.00414 (15158) covalent geometry : angle 0.63762 (21663) hydrogen bonds : bond 0.04450 ( 892) hydrogen bonds : angle 3.62085 ( 2280) metal coordination : bond 0.00850 ( 16) metal coordination : angle 11.13298 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2757.47 seconds wall clock time: 48 minutes 3.38 seconds (2883.38 seconds total)