Starting phenix.real_space_refine on Sat Aug 23 18:13:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sny_40642/08_2025/8sny_40642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sny_40642/08_2025/8sny_40642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sny_40642/08_2025/8sny_40642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sny_40642/08_2025/8sny_40642.map" model { file = "/net/cci-nas-00/data/ceres_data/8sny_40642/08_2025/8sny_40642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sny_40642/08_2025/8sny_40642.cif" } resolution = 3.41 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= 0.005 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 75 5.16 5 C 8733 2.51 5 N 2333 2.21 5 O 2595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1388, 11317 Classifications: {'peptide': 1388} Link IDs: {'PTRANS': 47, 'TRANS': 1340} Chain breaks: 3 Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "D" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 496 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain breaks: 1 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "T" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'RNA': 8} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 5} Time building chain proxies: 2.94, per 1000 atoms: 0.21 Number of scatterers: 13744 At special positions: 0 Unit cell: (123.786, 108.974, 108.974, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 8 15.00 O 2595 8.00 N 2333 7.00 C 8733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 483.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3218 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 8 sheets defined 62.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.725A pdb=" N LEU A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.679A pdb=" N LEU A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 98 through 132 removed outlier: 3.813A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 201 through 228 Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.782A pdb=" N LEU A 295 " --> pdb=" O CYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 325 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 349 through 380 removed outlier: 3.535A pdb=" N CYS A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.966A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.766A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.935A pdb=" N PHE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 509 through 518 removed outlier: 4.449A pdb=" N GLY A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.583A pdb=" N ILE A 549 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 4.399A pdb=" N LEU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 595 through 604 removed outlier: 3.776A pdb=" N ASN A 599 " --> pdb=" O CYS A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 651 Processing helix chain 'A' and resid 652 through 659 Proline residue: A 656 - end of helix removed outlier: 3.777A pdb=" N LEU A 659 " --> pdb=" O PRO A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.959A pdb=" N PHE A 708 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 724 removed outlier: 4.718A pdb=" N ILE A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 781 through 801 Processing helix chain 'A' and resid 832 through 852 Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 900 through 919 removed outlier: 3.743A pdb=" N GLU A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 939 Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 982 through 986 removed outlier: 3.538A pdb=" N PHE A 985 " --> pdb=" O PRO A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1003 through 1020 removed outlier: 4.300A pdb=" N GLU A1007 " --> pdb=" O ASP A1003 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1072 through 1087 removed outlier: 3.719A pdb=" N ILE A1076 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1099 Processing helix chain 'A' and resid 1099 through 1110 Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1130 through 1143 removed outlier: 3.861A pdb=" N ALA A1134 " --> pdb=" O PRO A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1174 Processing helix chain 'A' and resid 1175 through 1180 Processing helix chain 'A' and resid 1198 through 1212 Processing helix chain 'A' and resid 1223 through 1228 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1320 through 1326 removed outlier: 4.256A pdb=" N LYS A1326 " --> pdb=" O GLU A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1359 Processing helix chain 'A' and resid 1365 through 1375 Processing helix chain 'A' and resid 1384 through 1404 removed outlier: 3.514A pdb=" N CYS A1388 " --> pdb=" O VAL A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1419 Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1452 through 1457 Processing helix chain 'A' and resid 1458 through 1461 removed outlier: 3.952A pdb=" N LEU A1461 " --> pdb=" O GLU A1458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1458 through 1461' Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.570A pdb=" N ALA B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'C' and resid 129 through 157 removed outlier: 4.798A pdb=" N GLU C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 183 Processing helix chain 'D' and resid 129 through 158 Processing helix chain 'D' and resid 171 through 200 removed outlier: 3.570A pdb=" N MET D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 removed outlier: 4.050A pdb=" N ARG E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 191 through 200 Processing helix chain 'E' and resid 203 through 210 Processing helix chain 'E' and resid 217 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.319A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.543A pdb=" N VAL A 614 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 691 through 694 Processing sheet with id=AA6, first strand: chain 'A' and resid 812 through 815 Processing sheet with id=AA7, first strand: chain 'A' and resid 873 through 875 removed outlier: 3.845A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1361 through 1364 750 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2265 1.31 - 1.44: 3591 1.44 - 1.56: 8000 1.56 - 1.69: 15 1.69 - 1.81: 127 Bond restraints: 13998 Sorted by residual: bond pdb=" CA PHE A 704 " pdb=" C PHE A 704 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.30e-02 5.92e+03 2.50e+01 bond pdb=" CA MET A 631 " pdb=" C MET A 631 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.24e-02 6.50e+03 2.50e+01 bond pdb=" CA LYS A1145 " pdb=" C LYS A1145 " ideal model delta sigma weight residual 1.524 1.471 0.052 1.26e-02 6.30e+03 1.73e+01 bond pdb=" CA LEU A 673 " pdb=" C LEU A 673 " ideal model delta sigma weight residual 1.522 1.463 0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" CA GLN A 913 " pdb=" C GLN A 913 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.29e-02 6.01e+03 1.66e+01 ... (remaining 13993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 18717 2.43 - 4.85: 197 4.85 - 7.28: 22 7.28 - 9.71: 7 9.71 - 12.14: 3 Bond angle restraints: 18946 Sorted by residual: angle pdb=" N LEU A 667 " pdb=" CA LEU A 667 " pdb=" C LEU A 667 " ideal model delta sigma weight residual 111.02 98.88 12.14 1.22e+00 6.72e-01 9.90e+01 angle pdb=" N ALA A 675 " pdb=" CA ALA A 675 " pdb=" C ALA A 675 " ideal model delta sigma weight residual 111.07 102.61 8.46 1.07e+00 8.73e-01 6.25e+01 angle pdb=" N LEU A 673 " pdb=" CA LEU A 673 " pdb=" C LEU A 673 " ideal model delta sigma weight residual 112.90 103.68 9.22 1.31e+00 5.83e-01 4.95e+01 angle pdb=" N LYS A1025 " pdb=" CA LYS A1025 " pdb=" C LYS A1025 " ideal model delta sigma weight residual 114.04 105.99 8.05 1.24e+00 6.50e-01 4.21e+01 angle pdb=" C PHE A 704 " pdb=" CA PHE A 704 " pdb=" CB PHE A 704 " ideal model delta sigma weight residual 110.79 100.65 10.14 1.66e+00 3.63e-01 3.73e+01 ... (remaining 18941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7570 17.83 - 35.66: 811 35.66 - 53.49: 153 53.49 - 71.32: 36 71.32 - 89.15: 14 Dihedral angle restraints: 8584 sinusoidal: 3627 harmonic: 4957 Sorted by residual: dihedral pdb=" C PHE A 704 " pdb=" N PHE A 704 " pdb=" CA PHE A 704 " pdb=" CB PHE A 704 " ideal model delta harmonic sigma weight residual -122.60 -108.68 -13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" N PHE A 704 " pdb=" C PHE A 704 " pdb=" CA PHE A 704 " pdb=" CB PHE A 704 " ideal model delta harmonic sigma weight residual 122.80 112.96 9.84 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" CA GLN A 874 " pdb=" C GLN A 874 " pdb=" N HIS A 875 " pdb=" CA HIS A 875 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 8581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1847 0.055 - 0.110: 310 0.110 - 0.166: 35 0.166 - 0.221: 7 0.221 - 0.276: 2 Chirality restraints: 2201 Sorted by residual: chirality pdb=" CG LEU A 671 " pdb=" CB LEU A 671 " pdb=" CD1 LEU A 671 " pdb=" CD2 LEU A 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA LEU A 422 " pdb=" N LEU A 422 " pdb=" C LEU A 422 " pdb=" CB LEU A 422 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR A 93 " pdb=" CA THR A 93 " pdb=" OG1 THR A 93 " pdb=" CG2 THR A 93 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 2198 not shown) Planarity restraints: 2361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 707 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C ALA A 707 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA A 707 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 708 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 53 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 54 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 54 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 54 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 83 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.79e+00 pdb=" N PRO A 84 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " -0.027 5.00e-02 4.00e+02 ... (remaining 2358 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 116 2.53 - 3.12: 10875 3.12 - 3.71: 22625 3.71 - 4.31: 31221 4.31 - 4.90: 52711 Nonbonded interactions: 117548 Sorted by model distance: nonbonded pdb=" O ASN A 991 " pdb=" ND2 ASN A 991 " model vdw 1.932 3.120 nonbonded pdb=" O CYS A 251 " pdb=" OG1 THR A 264 " model vdw 2.216 3.040 nonbonded pdb=" OD1 ASP D 136 " pdb=" NH1 ARG E 134 " model vdw 2.242 3.120 nonbonded pdb=" NH2 ARG A 588 " pdb=" O LEU A1151 " model vdw 2.256 3.120 nonbonded pdb=" O VAL A1399 " pdb=" OG1 THR A1403 " model vdw 2.271 3.040 ... (remaining 117543 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 'B' and resid 130 through 184) selection = (chain 'C' and resid 130 through 184) } 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 0.800 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.480 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.004 0.065 13998 Z= 0.226 Angle : 0.625 12.136 18946 Z= 0.350 Chirality : 0.042 0.276 2201 Planarity : 0.004 0.049 2361 Dihedral : 15.353 89.155 5366 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.33 % Allowed : 0.85 % Favored : 98.83 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.21), residues: 1662 helix: 1.75 (0.17), residues: 955 sheet: -1.69 (0.55), residues: 72 loop : -0.86 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 167 TYR 0.021 0.001 TYR A1356 PHE 0.024 0.001 PHE A 704 TRP 0.015 0.002 TRP A 480 HIS 0.019 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00362 (13998) covalent geometry : angle 0.62492 (18946) hydrogen bonds : bond 0.10348 ( 750) hydrogen bonds : angle 5.07754 ( 2178) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 309 time to evaluate : 0.531 Fit side-chains REVERT: A 669 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7588 (pttp) REVERT: A 824 MET cc_start: 0.6091 (tmm) cc_final: 0.5831 (tmm) REVERT: A 1023 ASP cc_start: 0.6407 (m-30) cc_final: 0.6169 (t0) REVERT: B 152 LEU cc_start: 0.9017 (tp) cc_final: 0.8600 (tt) REVERT: C 140 GLU cc_start: 0.7632 (mp0) cc_final: 0.6963 (mp0) REVERT: C 177 MET cc_start: 0.8371 (tpp) cc_final: 0.8031 (tpp) REVERT: D 177 MET cc_start: 0.7450 (ppp) cc_final: 0.6904 (ppp) REVERT: D 178 ILE cc_start: 0.7151 (mm) cc_final: 0.6830 (mm) REVERT: E 145 ILE cc_start: 0.7918 (mt) cc_final: 0.7545 (mt) outliers start: 5 outliers final: 2 residues processed: 313 average time/residue: 0.0933 time to fit residues: 44.5113 Evaluate side-chains 241 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 674 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A 248 GLN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098874 restraints weight = 25238.133| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.15 r_work: 0.3062 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13998 Z= 0.207 Angle : 0.587 8.223 18946 Z= 0.305 Chirality : 0.043 0.165 2201 Planarity : 0.004 0.044 2361 Dihedral : 7.776 73.488 1966 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.82 % Allowed : 11.77 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.21), residues: 1662 helix: 1.52 (0.17), residues: 970 sheet: -1.68 (0.58), residues: 61 loop : -0.91 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 167 TYR 0.019 0.002 TYR A1356 PHE 0.021 0.002 PHE A 629 TRP 0.014 0.002 TRP A 480 HIS 0.017 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00484 (13998) covalent geometry : angle 0.58723 (18946) hydrogen bonds : bond 0.04077 ( 750) hydrogen bonds : angle 4.57740 ( 2178) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.519 Fit side-chains REVERT: A 565 TYR cc_start: 0.8724 (t80) cc_final: 0.8380 (t80) REVERT: A 669 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7535 (pttm) REVERT: A 1308 PHE cc_start: 0.7888 (t80) cc_final: 0.7669 (t80) REVERT: B 152 LEU cc_start: 0.9189 (tp) cc_final: 0.8771 (tt) REVERT: C 140 GLU cc_start: 0.8025 (mp0) cc_final: 0.7375 (mp0) REVERT: D 131 ILE cc_start: 0.6100 (mp) cc_final: 0.5820 (mp) REVERT: D 136 ASP cc_start: 0.7209 (m-30) cc_final: 0.6834 (t0) REVERT: D 177 MET cc_start: 0.7613 (ppp) cc_final: 0.7332 (ppp) REVERT: E 195 MET cc_start: 0.7472 (mtp) cc_final: 0.7167 (mtt) outliers start: 28 outliers final: 12 residues processed: 262 average time/residue: 0.0888 time to fit residues: 35.4026 Evaluate side-chains 234 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 222 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 175 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 59 optimal weight: 0.2980 chunk 73 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN A 248 GLN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 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 = 0.3528 r_free = 0.3528 target = 0.122304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102401 restraints weight = 25173.322| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.16 r_work: 0.3118 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13998 Z= 0.106 Angle : 0.498 7.751 18946 Z= 0.261 Chirality : 0.039 0.142 2201 Planarity : 0.003 0.053 2361 Dihedral : 7.551 73.424 1960 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.21 % Allowed : 14.37 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.21), residues: 1662 helix: 1.84 (0.16), residues: 954 sheet: -1.70 (0.56), residues: 69 loop : -0.71 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 182 TYR 0.016 0.001 TYR A1356 PHE 0.027 0.001 PHE A 87 TRP 0.014 0.001 TRP A 932 HIS 0.014 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00230 (13998) covalent geometry : angle 0.49847 (18946) hydrogen bonds : bond 0.03433 ( 750) hydrogen bonds : angle 4.32223 ( 2178) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 0.500 Fit side-chains REVERT: A 360 MET cc_start: 0.8048 (tpp) cc_final: 0.7848 (tpp) REVERT: A 440 MET cc_start: 0.8665 (mtp) cc_final: 0.8447 (mtm) REVERT: A 565 TYR cc_start: 0.8742 (t80) cc_final: 0.8330 (t80) REVERT: A 669 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7504 (pttm) REVERT: A 989 ASP cc_start: 0.8302 (t0) cc_final: 0.8066 (t0) REVERT: B 152 LEU cc_start: 0.9148 (tp) cc_final: 0.8738 (tt) REVERT: C 140 GLU cc_start: 0.8158 (mp0) cc_final: 0.7584 (mp0) REVERT: D 131 ILE cc_start: 0.6008 (mp) cc_final: 0.5712 (mp) REVERT: D 136 ASP cc_start: 0.7242 (m-30) cc_final: 0.6865 (t0) REVERT: E 220 SER cc_start: 0.8932 (m) cc_final: 0.8548 (m) outliers start: 34 outliers final: 20 residues processed: 286 average time/residue: 0.0824 time to fit residues: 36.2180 Evaluate side-chains 253 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 178 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 33 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099429 restraints weight = 25346.761| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.15 r_work: 0.3069 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13998 Z= 0.158 Angle : 0.523 7.568 18946 Z= 0.274 Chirality : 0.041 0.156 2201 Planarity : 0.004 0.049 2361 Dihedral : 7.564 73.369 1960 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.41 % Allowed : 17.23 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.21), residues: 1662 helix: 1.67 (0.16), residues: 965 sheet: -1.56 (0.57), residues: 61 loop : -0.72 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 182 TYR 0.014 0.001 TYR A 221 PHE 0.025 0.001 PHE A 87 TRP 0.012 0.002 TRP A 932 HIS 0.014 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00370 (13998) covalent geometry : angle 0.52284 (18946) hydrogen bonds : bond 0.03582 ( 750) hydrogen bonds : angle 4.38455 ( 2178) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 360 MET cc_start: 0.7940 (tpp) cc_final: 0.7642 (tpp) REVERT: A 483 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.7880 (pp) REVERT: A 565 TYR cc_start: 0.8826 (t80) cc_final: 0.8371 (t80) REVERT: A 669 LYS cc_start: 0.8201 (mtmt) cc_final: 0.7559 (pttm) REVERT: A 989 ASP cc_start: 0.8322 (t0) cc_final: 0.8021 (t0) REVERT: A 1135 GLU cc_start: 0.8518 (tt0) cc_final: 0.8210 (tt0) REVERT: A 1229 ASP cc_start: 0.7951 (t70) cc_final: 0.7723 (t70) REVERT: A 1372 LEU cc_start: 0.8209 (mt) cc_final: 0.7952 (mp) REVERT: A 1445 MET cc_start: 0.8615 (pmm) cc_final: 0.8378 (pmm) REVERT: B 152 LEU cc_start: 0.9198 (tp) cc_final: 0.8781 (tt) REVERT: B 175 GLU cc_start: 0.8369 (mp0) cc_final: 0.8114 (mt-10) REVERT: C 140 GLU cc_start: 0.8035 (mp0) cc_final: 0.7548 (mp0) REVERT: D 131 ILE cc_start: 0.6061 (mp) cc_final: 0.5730 (mp) REVERT: D 136 ASP cc_start: 0.7217 (m-30) cc_final: 0.6817 (t0) REVERT: E 177 MET cc_start: 0.8351 (mtp) cc_final: 0.8089 (mtp) REVERT: E 220 SER cc_start: 0.9061 (m) cc_final: 0.8808 (m) outliers start: 37 outliers final: 27 residues processed: 258 average time/residue: 0.0944 time to fit residues: 37.2113 Evaluate side-chains 254 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.0270 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 ASN A 853 HIS ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.121274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101071 restraints weight = 25208.756| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.17 r_work: 0.3096 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13998 Z= 0.119 Angle : 0.494 8.499 18946 Z= 0.260 Chirality : 0.040 0.160 2201 Planarity : 0.003 0.051 2361 Dihedral : 7.480 73.329 1960 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.99 % Allowed : 18.27 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.21), residues: 1662 helix: 1.73 (0.16), residues: 967 sheet: -1.50 (0.57), residues: 61 loop : -0.67 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 167 TYR 0.013 0.001 TYR A 221 PHE 0.015 0.001 PHE A 629 TRP 0.013 0.001 TRP A 932 HIS 0.014 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00272 (13998) covalent geometry : angle 0.49429 (18946) hydrogen bonds : bond 0.03382 ( 750) hydrogen bonds : angle 4.29068 ( 2178) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8323 (t80) cc_final: 0.8083 (t80) REVERT: A 131 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8624 (mp) REVERT: A 340 MET cc_start: 0.8680 (tpt) cc_final: 0.8274 (tpt) REVERT: A 440 MET cc_start: 0.8739 (mtp) cc_final: 0.8506 (mtm) REVERT: A 483 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.7845 (pp) REVERT: A 565 TYR cc_start: 0.8859 (t80) cc_final: 0.8397 (t80) REVERT: A 989 ASP cc_start: 0.8300 (t0) cc_final: 0.8037 (t0) REVERT: A 1026 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7332 (p0) REVERT: A 1135 GLU cc_start: 0.8482 (tt0) cc_final: 0.8207 (tt0) REVERT: B 134 ARG cc_start: 0.7418 (ptm160) cc_final: 0.6706 (mtp-110) REVERT: B 140 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8089 (mt-10) REVERT: B 152 LEU cc_start: 0.9173 (tp) cc_final: 0.8755 (tt) REVERT: C 140 GLU cc_start: 0.8137 (mp0) cc_final: 0.7865 (mp0) REVERT: D 131 ILE cc_start: 0.6057 (mp) cc_final: 0.5719 (mp) REVERT: D 136 ASP cc_start: 0.7241 (m-30) cc_final: 0.6815 (t0) outliers start: 46 outliers final: 34 residues processed: 286 average time/residue: 0.0923 time to fit residues: 40.3353 Evaluate side-chains 268 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 106 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 ASN ** 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 = 0.3464 r_free = 0.3464 target = 0.118136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097851 restraints weight = 25258.477| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.14 r_work: 0.3040 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13998 Z= 0.186 Angle : 0.556 7.966 18946 Z= 0.291 Chirality : 0.042 0.189 2201 Planarity : 0.004 0.046 2361 Dihedral : 7.623 73.443 1960 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.84 % Allowed : 18.92 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.21), residues: 1662 helix: 1.53 (0.16), residues: 966 sheet: -1.51 (0.55), residues: 61 loop : -0.74 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 167 TYR 0.018 0.001 TYR A 266 PHE 0.020 0.002 PHE A 629 TRP 0.011 0.002 TRP A 932 HIS 0.015 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00437 (13998) covalent geometry : angle 0.55555 (18946) hydrogen bonds : bond 0.03739 ( 750) hydrogen bonds : angle 4.45604 ( 2178) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 225 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8436 (t80) cc_final: 0.8199 (t80) REVERT: A 92 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8369 (mmp) REVERT: A 131 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8679 (mp) REVERT: A 459 SER cc_start: 0.9104 (t) cc_final: 0.8848 (t) REVERT: A 483 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8001 (pp) REVERT: A 565 TYR cc_start: 0.8921 (t80) cc_final: 0.8436 (t80) REVERT: A 875 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.6905 (p90) REVERT: A 989 ASP cc_start: 0.8519 (t0) cc_final: 0.8256 (t0) REVERT: A 1135 GLU cc_start: 0.8786 (tt0) cc_final: 0.8486 (tt0) REVERT: A 1229 ASP cc_start: 0.8175 (t70) cc_final: 0.7948 (m-30) REVERT: B 152 LEU cc_start: 0.9256 (tp) cc_final: 0.8819 (tt) REVERT: C 140 GLU cc_start: 0.8284 (mp0) cc_final: 0.7995 (mp0) REVERT: D 131 ILE cc_start: 0.6167 (mp) cc_final: 0.5733 (mp) outliers start: 59 outliers final: 39 residues processed: 262 average time/residue: 0.0818 time to fit residues: 33.1618 Evaluate side-chains 263 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 ASN ** 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 = 0.3452 r_free = 0.3452 target = 0.117299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.097268 restraints weight = 25112.412| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.11 r_work: 0.3024 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13998 Z= 0.214 Angle : 0.579 8.159 18946 Z= 0.303 Chirality : 0.043 0.176 2201 Planarity : 0.004 0.045 2361 Dihedral : 7.711 73.504 1960 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.38 % Allowed : 20.09 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.21), residues: 1662 helix: 1.38 (0.16), residues: 967 sheet: -1.63 (0.54), residues: 61 loop : -0.86 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 167 TYR 0.017 0.002 TYR A 266 PHE 0.023 0.002 PHE A 629 TRP 0.012 0.002 TRP A 932 HIS 0.015 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00507 (13998) covalent geometry : angle 0.57941 (18946) hydrogen bonds : bond 0.03877 ( 750) hydrogen bonds : angle 4.53143 ( 2178) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 459 SER cc_start: 0.9166 (t) cc_final: 0.8926 (t) REVERT: A 483 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8016 (pp) REVERT: A 565 TYR cc_start: 0.8942 (t80) cc_final: 0.8441 (t80) REVERT: A 816 ASP cc_start: 0.8443 (t0) cc_final: 0.8126 (t70) REVERT: A 875 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7091 (p90) REVERT: A 1135 GLU cc_start: 0.8801 (tt0) cc_final: 0.8415 (tt0) REVERT: A 1229 ASP cc_start: 0.8186 (t70) cc_final: 0.7970 (m-30) REVERT: B 134 ARG cc_start: 0.7779 (ptm160) cc_final: 0.7097 (ttt-90) REVERT: B 152 LEU cc_start: 0.9262 (tp) cc_final: 0.8839 (tt) REVERT: C 140 GLU cc_start: 0.8218 (mp0) cc_final: 0.7985 (mp0) REVERT: D 131 ILE cc_start: 0.6185 (mp) cc_final: 0.5758 (mp) outliers start: 52 outliers final: 40 residues processed: 250 average time/residue: 0.0951 time to fit residues: 36.4919 Evaluate side-chains 258 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 88 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 ASN ** 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 = 0.3465 r_free = 0.3465 target = 0.118119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.097990 restraints weight = 24942.122| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.12 r_work: 0.3047 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13998 Z= 0.165 Angle : 0.548 7.796 18946 Z= 0.287 Chirality : 0.042 0.182 2201 Planarity : 0.004 0.045 2361 Dihedral : 7.670 73.434 1960 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.19 % Allowed : 21.07 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.21), residues: 1662 helix: 1.44 (0.16), residues: 966 sheet: -1.50 (0.55), residues: 61 loop : -0.85 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 167 TYR 0.017 0.001 TYR A 266 PHE 0.026 0.002 PHE A 629 TRP 0.013 0.002 TRP A 203 HIS 0.018 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00388 (13998) covalent geometry : angle 0.54813 (18946) hydrogen bonds : bond 0.03698 ( 750) hydrogen bonds : angle 4.46790 ( 2178) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8733 (mp) REVERT: A 360 MET cc_start: 0.8197 (tpp) cc_final: 0.7848 (tpp) REVERT: A 459 SER cc_start: 0.9119 (t) cc_final: 0.8884 (t) REVERT: A 483 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8049 (pp) REVERT: A 565 TYR cc_start: 0.8949 (t80) cc_final: 0.8456 (t80) REVERT: A 875 HIS cc_start: 0.7760 (OUTLIER) cc_final: 0.7010 (p90) REVERT: A 1135 GLU cc_start: 0.8777 (tt0) cc_final: 0.8402 (tt0) REVERT: A 1229 ASP cc_start: 0.8193 (t70) cc_final: 0.7976 (m-30) REVERT: A 1422 MET cc_start: 0.7754 (ptt) cc_final: 0.7477 (ptt) REVERT: B 152 LEU cc_start: 0.9248 (tp) cc_final: 0.8817 (tt) REVERT: C 140 GLU cc_start: 0.8220 (mp0) cc_final: 0.7992 (mp0) REVERT: D 131 ILE cc_start: 0.6181 (mp) cc_final: 0.5755 (mp) outliers start: 49 outliers final: 36 residues processed: 262 average time/residue: 0.1044 time to fit residues: 41.6223 Evaluate side-chains 257 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 0.0070 chunk 61 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 151 optimal weight: 30.0000 chunk 81 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 overall best weight: 2.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 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 = 0.3460 r_free = 0.3460 target = 0.117771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097695 restraints weight = 25219.160| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.13 r_work: 0.3045 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13998 Z= 0.169 Angle : 0.564 8.935 18946 Z= 0.293 Chirality : 0.042 0.185 2201 Planarity : 0.004 0.045 2361 Dihedral : 7.678 73.435 1960 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.12 % Allowed : 21.46 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.21), residues: 1662 helix: 1.44 (0.16), residues: 966 sheet: -1.50 (0.55), residues: 61 loop : -0.85 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 167 TYR 0.016 0.001 TYR A 266 PHE 0.017 0.002 PHE A 629 TRP 0.018 0.002 TRP A 203 HIS 0.017 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00401 (13998) covalent geometry : angle 0.56447 (18946) hydrogen bonds : bond 0.03733 ( 750) hydrogen bonds : angle 4.46773 ( 2178) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8748 (mp) REVERT: A 360 MET cc_start: 0.8196 (tpp) cc_final: 0.7611 (tpp) REVERT: A 376 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9143 (mm) REVERT: A 459 SER cc_start: 0.9136 (t) cc_final: 0.8891 (t) REVERT: A 483 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8036 (pp) REVERT: A 565 TYR cc_start: 0.8947 (t80) cc_final: 0.8459 (t80) REVERT: A 875 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7057 (p90) REVERT: A 1135 GLU cc_start: 0.8780 (tt0) cc_final: 0.8406 (tt0) REVERT: A 1229 ASP cc_start: 0.8152 (t70) cc_final: 0.7886 (m-30) REVERT: A 1309 MET cc_start: 0.7765 (mmt) cc_final: 0.7523 (mmt) REVERT: A 1422 MET cc_start: 0.7753 (ptt) cc_final: 0.7477 (ptt) REVERT: B 134 ARG cc_start: 0.7611 (ptm160) cc_final: 0.6807 (mtp-110) REVERT: B 152 LEU cc_start: 0.9236 (tp) cc_final: 0.8810 (tt) REVERT: C 140 GLU cc_start: 0.8207 (mp0) cc_final: 0.7942 (mp0) REVERT: D 131 ILE cc_start: 0.6190 (mp) cc_final: 0.5759 (mp) REVERT: E 177 MET cc_start: 0.8179 (mtp) cc_final: 0.7838 (mtp) outliers start: 48 outliers final: 42 residues processed: 255 average time/residue: 0.1069 time to fit residues: 41.2614 Evaluate side-chains 263 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain A residue 1419 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 217 ASN Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 0.4980 chunk 163 optimal weight: 0.5980 chunk 110 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 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 248 GLN A 640 GLN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 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 = 0.3520 r_free = 0.3520 target = 0.121904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101818 restraints weight = 25053.289| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.14 r_work: 0.3110 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13998 Z= 0.109 Angle : 0.523 8.634 18946 Z= 0.272 Chirality : 0.040 0.191 2201 Planarity : 0.004 0.051 2361 Dihedral : 7.406 73.329 1960 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.47 % Allowed : 22.24 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.21), residues: 1662 helix: 1.67 (0.16), residues: 964 sheet: -1.35 (0.54), residues: 69 loop : -0.77 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 167 TYR 0.016 0.001 TYR A 266 PHE 0.043 0.001 PHE A 629 TRP 0.020 0.002 TRP A 203 HIS 0.017 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00241 (13998) covalent geometry : angle 0.52335 (18946) hydrogen bonds : bond 0.03341 ( 750) hydrogen bonds : angle 4.31508 ( 2178) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 247 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.8294 (mmp) cc_final: 0.8070 (mmp) REVERT: A 131 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8679 (mp) REVERT: A 333 LYS cc_start: 0.8822 (tttp) cc_final: 0.8348 (ttmm) REVERT: A 348 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7216 (mm-30) REVERT: A 360 MET cc_start: 0.7877 (tpp) cc_final: 0.7369 (tpp) REVERT: A 376 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9122 (mm) REVERT: A 483 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.7895 (pp) REVERT: A 565 TYR cc_start: 0.8831 (t80) cc_final: 0.8316 (t80) REVERT: A 1135 GLU cc_start: 0.8496 (tt0) cc_final: 0.8189 (tt0) REVERT: B 134 ARG cc_start: 0.7446 (ptm160) cc_final: 0.6675 (mtp-110) REVERT: B 140 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8048 (mt-10) REVERT: B 152 LEU cc_start: 0.9097 (tp) cc_final: 0.8660 (tt) REVERT: D 131 ILE cc_start: 0.6196 (mp) cc_final: 0.5810 (mp) REVERT: E 177 MET cc_start: 0.8017 (mtp) cc_final: 0.7595 (mtp) outliers start: 38 outliers final: 29 residues processed: 272 average time/residue: 0.1066 time to fit residues: 43.8829 Evaluate side-chains 258 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 217 ASN Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 81 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 114 optimal weight: 0.0980 chunk 111 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100560 restraints weight = 25041.197| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.13 r_work: 0.3088 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13998 Z= 0.130 Angle : 0.552 8.290 18946 Z= 0.289 Chirality : 0.041 0.268 2201 Planarity : 0.004 0.052 2361 Dihedral : 7.419 73.356 1960 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.86 % Allowed : 21.98 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.21), residues: 1662 helix: 1.59 (0.16), residues: 970 sheet: -1.12 (0.57), residues: 61 loop : -0.71 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 167 TYR 0.037 0.001 TYR A 34 PHE 0.029 0.001 PHE A 629 TRP 0.019 0.002 TRP A 203 HIS 0.017 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00303 (13998) covalent geometry : angle 0.55235 (18946) hydrogen bonds : bond 0.03494 ( 750) hydrogen bonds : angle 4.35600 ( 2178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.38 seconds wall clock time: 46 minutes 48.27 seconds (2808.27 seconds total)