Starting phenix.real_space_refine on Fri May 16 01:30:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sny_40642/05_2025/8sny_40642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sny_40642/05_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_40642/05_2025/8sny_40642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sny_40642/05_2025/8sny_40642.map" model { file = "/net/cci-nas-00/data/ceres_data/8sny_40642/05_2025/8sny_40642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sny_40642/05_2025/8sny_40642.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.91, per 1000 atoms: 0.58 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: 3.52 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.75 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: 4.99 Time building geometry restraints manager: 4.07 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: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.020 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.550 ------------------------------------------------------------------------------- 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 : 13.38 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.002 TRP A 480 HIS 0.019 0.001 HIS C 150 PHE 0.024 0.001 PHE A 704 TYR 0.021 0.001 TYR A1356 ARG 0.009 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.10348 ( 750) hydrogen bonds : angle 5.07754 ( 2178) covalent geometry : bond 0.00362 (13998) covalent geometry : angle 0.62492 (18946) *********************** 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 : 1.671 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: 0.2418 time to fit residues: 112.9530 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 : 1.457 ------------------------------------------------------------------------------- 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 139 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 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 229 HIS ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3493 r_free = 0.3493 target = 0.119855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099775 restraints weight = 25029.902| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.14 r_work: 0.3079 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13998 Z= 0.194 Angle : 0.577 8.067 18946 Z= 0.300 Chirality : 0.043 0.170 2201 Planarity : 0.004 0.045 2361 Dihedral : 7.740 73.527 1966 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.76 % Allowed : 11.18 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1662 helix: 1.58 (0.17), residues: 971 sheet: -1.64 (0.59), residues: 61 loop : -0.88 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 932 HIS 0.017 0.001 HIS C 150 PHE 0.023 0.002 PHE A 629 TYR 0.020 0.002 TYR A1356 ARG 0.005 0.001 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 750) hydrogen bonds : angle 4.54579 ( 2178) covalent geometry : bond 0.00455 (13998) covalent geometry : angle 0.57651 (18946) *********************** 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 278 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 1.520 Fit side-chains REVERT: A 565 TYR cc_start: 0.8707 (t80) cc_final: 0.8348 (t80) REVERT: A 669 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7484 (pttm) REVERT: A 1308 PHE cc_start: 0.7843 (t80) cc_final: 0.7633 (t80) REVERT: B 152 LEU cc_start: 0.9158 (tp) cc_final: 0.8744 (tt) REVERT: C 140 GLU cc_start: 0.8027 (mp0) cc_final: 0.7376 (mp0) REVERT: D 131 ILE cc_start: 0.6027 (mp) cc_final: 0.5749 (mp) REVERT: D 136 ASP cc_start: 0.7217 (m-30) cc_final: 0.6836 (t0) REVERT: D 177 MET cc_start: 0.7623 (ppp) cc_final: 0.7336 (ppp) REVERT: E 195 MET cc_start: 0.7488 (mtp) cc_final: 0.7158 (mtt) outliers start: 27 outliers final: 12 residues processed: 263 average time/residue: 0.2404 time to fit residues: 94.9949 Evaluate side-chains 238 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 226 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 835 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 895 ASN 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 119 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 chunk 91 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A 991 ASN ** 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 = 0.3519 r_free = 0.3519 target = 0.121787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101928 restraints weight = 25110.056| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.16 r_work: 0.3112 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 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 = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1437 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= 0.118 Angle : 0.505 7.817 18946 Z= 0.265 Chirality : 0.040 0.141 2201 Planarity : 0.004 0.051 2361 Dihedral : 7.571 73.406 1960 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.89 % Allowed : 14.24 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1662 helix: 1.81 (0.16), residues: 954 sheet: -1.73 (0.55), residues: 69 loop : -0.71 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 932 HIS 0.014 0.001 HIS C 150 PHE 0.027 0.001 PHE A 87 TYR 0.015 0.001 TYR A1356 ARG 0.006 0.000 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 750) hydrogen bonds : angle 4.35903 ( 2178) covalent geometry : bond 0.00265 (13998) covalent geometry : angle 0.50529 (18946) *********************** 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 296 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 1.443 Fit side-chains REVERT: A 440 MET cc_start: 0.8711 (mtp) cc_final: 0.8499 (mtm) REVERT: A 565 TYR cc_start: 0.8738 (t80) cc_final: 0.8347 (t80) REVERT: A 669 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7513 (pttm) REVERT: A 989 ASP cc_start: 0.8325 (t0) cc_final: 0.8059 (t0) REVERT: A 1135 GLU cc_start: 0.8484 (tt0) cc_final: 0.8254 (tt0) REVERT: A 1372 LEU cc_start: 0.8024 (mm) cc_final: 0.7814 (mp) REVERT: A 1376 TYR cc_start: 0.7299 (m-80) cc_final: 0.6920 (m-80) REVERT: A 1445 MET cc_start: 0.8561 (pmm) cc_final: 0.8284 (pmm) REVERT: B 152 LEU cc_start: 0.9130 (tp) cc_final: 0.8682 (tt) REVERT: C 140 GLU cc_start: 0.8137 (mp0) cc_final: 0.7554 (mp0) REVERT: C 152 LEU cc_start: 0.8942 (mt) cc_final: 0.8719 (mp) REVERT: D 131 ILE cc_start: 0.6017 (mp) cc_final: 0.5717 (mp) REVERT: D 136 ASP cc_start: 0.7191 (m-30) cc_final: 0.6810 (t0) REVERT: E 220 SER cc_start: 0.8941 (m) cc_final: 0.8553 (m) outliers start: 29 outliers final: 20 residues processed: 281 average time/residue: 0.2399 time to fit residues: 101.7267 Evaluate side-chains 247 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 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 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 156 SER Chi-restraints excluded: chain E residue 175 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 114 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A 991 ASN ** 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 = 0.3492 r_free = 0.3492 target = 0.119955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099828 restraints weight = 24984.141| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.13 r_work: 0.3077 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13998 Z= 0.151 Angle : 0.524 7.555 18946 Z= 0.274 Chirality : 0.041 0.157 2201 Planarity : 0.004 0.049 2361 Dihedral : 7.568 73.366 1960 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.41 % Allowed : 16.91 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1662 helix: 1.71 (0.16), residues: 959 sheet: -1.55 (0.57), residues: 61 loop : -0.71 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 932 HIS 0.015 0.001 HIS C 150 PHE 0.014 0.001 PHE A 424 TYR 0.014 0.001 TYR A 221 ARG 0.005 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 750) hydrogen bonds : angle 4.38239 ( 2178) covalent geometry : bond 0.00351 (13998) covalent geometry : angle 0.52433 (18946) *********************** 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 277 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 1.661 Fit side-chains revert: symmetry clash REVERT: A 483 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.7980 (pp) REVERT: A 565 TYR cc_start: 0.8872 (t80) cc_final: 0.8401 (t80) REVERT: A 669 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7507 (pttm) REVERT: A 989 ASP cc_start: 0.8502 (t0) cc_final: 0.8203 (t0) REVERT: A 1135 GLU cc_start: 0.8747 (tt0) cc_final: 0.8453 (tt0) REVERT: A 1372 LEU cc_start: 0.8128 (mm) cc_final: 0.7886 (mp) REVERT: A 1445 MET cc_start: 0.8770 (pmm) cc_final: 0.8509 (pmm) REVERT: B 152 LEU cc_start: 0.9220 (tp) cc_final: 0.8813 (tt) REVERT: C 140 GLU cc_start: 0.8176 (mp0) cc_final: 0.7675 (mp0) REVERT: D 131 ILE cc_start: 0.6070 (mp) cc_final: 0.5722 (mp) REVERT: D 136 ASP cc_start: 0.7302 (m-30) cc_final: 0.6879 (t0) REVERT: E 220 SER cc_start: 0.8997 (m) cc_final: 0.8621 (m) outliers start: 37 outliers final: 29 residues processed: 258 average time/residue: 0.2353 time to fit residues: 92.5249 Evaluate side-chains 258 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 487 ILE 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 628 MET Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 763 VAL 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 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 171 VAL 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 100 optimal weight: 3.9990 chunk 118 optimal weight: 0.0670 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 4 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN 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 = 0.3534 r_free = 0.3534 target = 0.122724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102804 restraints weight = 24903.060| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.15 r_work: 0.3123 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1716 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= 0.103 Angle : 0.487 8.701 18946 Z= 0.255 Chirality : 0.039 0.159 2201 Planarity : 0.003 0.053 2361 Dihedral : 7.427 73.382 1960 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.21 % Allowed : 19.18 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1662 helix: 1.78 (0.16), residues: 968 sheet: -1.40 (0.56), residues: 61 loop : -0.62 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 932 HIS 0.015 0.001 HIS C 150 PHE 0.022 0.001 PHE A 87 TYR 0.014 0.001 TYR A 221 ARG 0.006 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 750) hydrogen bonds : angle 4.24906 ( 2178) covalent geometry : bond 0.00226 (13998) covalent geometry : angle 0.48738 (18946) *********************** 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 306 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 272 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8295 (t80) cc_final: 0.8070 (t80) REVERT: A 131 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 340 MET cc_start: 0.8555 (tpt) cc_final: 0.8102 (tpt) REVERT: A 440 MET cc_start: 0.8724 (mtp) cc_final: 0.8491 (mtm) REVERT: A 483 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7844 (pp) REVERT: A 565 TYR cc_start: 0.8852 (t80) cc_final: 0.8366 (t80) REVERT: A 669 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7425 (pttm) REVERT: A 979 MET cc_start: 0.8890 (mmm) cc_final: 0.8583 (mmp) REVERT: A 989 ASP cc_start: 0.8239 (t0) cc_final: 0.7975 (t0) REVERT: A 1135 GLU cc_start: 0.8464 (tt0) cc_final: 0.8243 (tt0) REVERT: B 134 ARG cc_start: 0.7401 (ptm160) cc_final: 0.6663 (mtp-110) REVERT: B 152 LEU cc_start: 0.9129 (tp) cc_final: 0.8744 (tt) REVERT: C 140 GLU cc_start: 0.8160 (mp0) cc_final: 0.7870 (mp0) REVERT: D 131 ILE cc_start: 0.6051 (mp) cc_final: 0.5730 (mp) REVERT: D 136 ASP cc_start: 0.7317 (m-30) cc_final: 0.6878 (t0) REVERT: E 136 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.7091 (t0) REVERT: E 220 SER cc_start: 0.8917 (m) cc_final: 0.8514 (m) outliers start: 34 outliers final: 21 residues processed: 291 average time/residue: 0.2368 time to fit residues: 105.1675 Evaluate side-chains 266 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 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 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 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 D residue 152 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL 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 16 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS ** 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 = 0.3524 r_free = 0.3524 target = 0.122087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.102106 restraints weight = 25219.300| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.16 r_work: 0.3113 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 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 = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13998 Z= 0.115 Angle : 0.514 9.788 18946 Z= 0.264 Chirality : 0.040 0.179 2201 Planarity : 0.003 0.053 2361 Dihedral : 7.410 73.328 1960 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.93 % Allowed : 19.38 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.21), residues: 1662 helix: 1.78 (0.16), residues: 968 sheet: -1.36 (0.56), residues: 61 loop : -0.60 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 932 HIS 0.015 0.001 HIS C 150 PHE 0.027 0.001 PHE A 629 TYR 0.014 0.001 TYR A 221 ARG 0.008 0.000 ARG C 182 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 750) hydrogen bonds : angle 4.27081 ( 2178) covalent geometry : bond 0.00262 (13998) covalent geometry : angle 0.51354 (18946) *********************** 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 293 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8280 (t80) cc_final: 0.8058 (t80) REVERT: A 92 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7990 (mmp) REVERT: A 131 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8525 (mp) REVERT: A 340 MET cc_start: 0.8599 (tpt) cc_final: 0.8156 (tpp) REVERT: A 483 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.7858 (pp) REVERT: A 565 TYR cc_start: 0.8852 (t80) cc_final: 0.8352 (t80) REVERT: A 669 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7352 (pttm) REVERT: A 1026 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7157 (p0) REVERT: A 1135 GLU cc_start: 0.8478 (tt0) cc_final: 0.8231 (tt0) REVERT: B 152 LEU cc_start: 0.9136 (tp) cc_final: 0.8736 (tt) REVERT: C 140 GLU cc_start: 0.8153 (mp0) cc_final: 0.7850 (mp0) REVERT: D 131 ILE cc_start: 0.6136 (mp) cc_final: 0.5738 (mp) REVERT: E 220 SER cc_start: 0.8941 (m) cc_final: 0.8528 (m) outliers start: 45 outliers final: 31 residues processed: 273 average time/residue: 0.2388 time to fit residues: 98.8921 Evaluate side-chains 271 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 379 VAL 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 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 851 ILE Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 948 ASN 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 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 A residue 1413 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 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 156 SER Chi-restraints excluded: chain E residue 171 VAL 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 128 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 75 optimal weight: 0.0270 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 overall best weight: 2.3642 ------------------------------------------------------------------------------- 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 243 GLN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099384 restraints weight = 25171.343| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.12 r_work: 0.3068 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 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 = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13998 Z= 0.164 Angle : 0.546 7.792 18946 Z= 0.283 Chirality : 0.041 0.190 2201 Planarity : 0.004 0.050 2361 Dihedral : 7.548 73.384 1960 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.93 % Allowed : 19.96 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1662 helix: 1.61 (0.16), residues: 966 sheet: -1.43 (0.55), residues: 61 loop : -0.65 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 203 HIS 0.015 0.001 HIS C 150 PHE 0.022 0.002 PHE A 629 TYR 0.014 0.001 TYR A 221 ARG 0.006 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 750) hydrogen bonds : angle 4.41015 ( 2178) covalent geometry : bond 0.00385 (13998) covalent geometry : angle 0.54607 (18946) *********************** 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 288 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8408 (t80) cc_final: 0.8181 (t80) REVERT: A 92 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8377 (mmp) REVERT: A 131 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 340 MET cc_start: 0.8650 (tpt) cc_final: 0.8318 (tpp) REVERT: A 440 MET cc_start: 0.8829 (mtp) cc_final: 0.8569 (mtm) REVERT: A 459 SER cc_start: 0.9111 (t) cc_final: 0.8857 (t) REVERT: A 483 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.7916 (pp) REVERT: A 565 TYR cc_start: 0.8917 (t80) cc_final: 0.8414 (t80) REVERT: A 875 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.6915 (p90) REVERT: A 1135 GLU cc_start: 0.8783 (tt0) cc_final: 0.8454 (tt0) REVERT: B 134 ARG cc_start: 0.7478 (ptm160) cc_final: 0.6820 (mtp-110) REVERT: B 152 LEU cc_start: 0.9217 (tp) cc_final: 0.8813 (tt) REVERT: C 140 GLU cc_start: 0.8273 (mp0) cc_final: 0.7975 (mp0) REVERT: D 131 ILE cc_start: 0.6063 (mp) cc_final: 0.5678 (mp) REVERT: E 220 SER cc_start: 0.9016 (m) cc_final: 0.8682 (m) outliers start: 45 outliers final: 33 residues processed: 270 average time/residue: 0.2350 time to fit residues: 96.7463 Evaluate side-chains 270 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 1.670 ------------------------------------------------------------------------------- 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 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE 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 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 D residue 152 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS ** 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 = 0.3494 r_free = 0.3494 target = 0.120263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100397 restraints weight = 25097.673| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.13 r_work: 0.3077 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 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 = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13998 Z= 0.134 Angle : 0.530 8.126 18946 Z= 0.275 Chirality : 0.040 0.186 2201 Planarity : 0.003 0.052 2361 Dihedral : 7.519 73.372 1960 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.67 % Allowed : 20.48 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1662 helix: 1.63 (0.16), residues: 964 sheet: -1.46 (0.56), residues: 61 loop : -0.68 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 203 HIS 0.017 0.001 HIS C 150 PHE 0.025 0.001 PHE A 629 TYR 0.020 0.001 TYR A 266 ARG 0.008 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 750) hydrogen bonds : angle 4.39135 ( 2178) covalent geometry : bond 0.00311 (13998) covalent geometry : angle 0.52965 (18946) *********************** 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 279 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8378 (t80) cc_final: 0.8046 (t80) REVERT: A 92 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8275 (mmp) REVERT: A 131 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8610 (mp) REVERT: A 483 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.7933 (pp) REVERT: A 565 TYR cc_start: 0.8935 (t80) cc_final: 0.8417 (t80) REVERT: A 875 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.6765 (p90) REVERT: A 989 ASP cc_start: 0.8460 (t0) cc_final: 0.8228 (t0) REVERT: A 1135 GLU cc_start: 0.8774 (tt0) cc_final: 0.8458 (tt0) REVERT: B 134 ARG cc_start: 0.7497 (ptm160) cc_final: 0.6786 (mtp-110) REVERT: B 152 LEU cc_start: 0.9207 (tp) cc_final: 0.8810 (tt) REVERT: C 140 GLU cc_start: 0.8281 (mp0) cc_final: 0.7980 (mp0) REVERT: D 131 ILE cc_start: 0.6159 (mp) cc_final: 0.5766 (mp) REVERT: E 220 SER cc_start: 0.9014 (m) cc_final: 0.8721 (m) outliers start: 41 outliers final: 32 residues processed: 261 average time/residue: 0.2414 time to fit residues: 96.9583 Evaluate side-chains 263 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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 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 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 742 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 847 GLU 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 972 ASP Chi-restraints excluded: chain A residue 983 MET 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 A residue 1413 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 152 LEU 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 239 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 117 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 243 GLN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.098526 restraints weight = 25006.623| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.10 r_work: 0.3057 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 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 = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13998 Z= 0.175 Angle : 0.564 8.242 18946 Z= 0.294 Chirality : 0.042 0.200 2201 Planarity : 0.004 0.048 2361 Dihedral : 7.615 73.435 1960 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.80 % Allowed : 20.94 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1662 helix: 1.48 (0.16), residues: 966 sheet: -1.51 (0.54), residues: 61 loop : -0.73 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 203 HIS 0.017 0.001 HIS C 150 PHE 0.026 0.002 PHE A 629 TYR 0.019 0.001 TYR A 746 ARG 0.009 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 750) hydrogen bonds : angle 4.47596 ( 2178) covalent geometry : bond 0.00413 (13998) covalent geometry : angle 0.56404 (18946) *********************** 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 275 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8604 (mp) REVERT: A 459 SER cc_start: 0.9143 (t) cc_final: 0.8899 (t) REVERT: A 483 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.7919 (pp) REVERT: A 565 TYR cc_start: 0.8938 (t80) cc_final: 0.8437 (t80) REVERT: A 875 HIS cc_start: 0.7760 (OUTLIER) cc_final: 0.6846 (p90) REVERT: A 1135 GLU cc_start: 0.8784 (tt0) cc_final: 0.8475 (tt0) REVERT: A 1309 MET cc_start: 0.7750 (mmt) cc_final: 0.7457 (mmt) REVERT: A 1422 MET cc_start: 0.7698 (ptt) cc_final: 0.7348 (ptt) REVERT: B 152 LEU cc_start: 0.9229 (tp) cc_final: 0.8829 (tt) REVERT: C 140 GLU cc_start: 0.8176 (mp0) cc_final: 0.7933 (mp0) REVERT: D 131 ILE cc_start: 0.6216 (mp) cc_final: 0.5810 (mp) REVERT: E 220 SER cc_start: 0.9093 (m) cc_final: 0.8843 (m) outliers start: 43 outliers final: 34 residues processed: 257 average time/residue: 0.2416 time to fit residues: 93.7222 Evaluate side-chains 260 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 295 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 487 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL 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 847 GLU 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 983 MET 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 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 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 8 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.098591 restraints weight = 25249.293| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.13 r_work: 0.3054 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13998 Z= 0.166 Angle : 0.560 8.029 18946 Z= 0.294 Chirality : 0.042 0.190 2201 Planarity : 0.004 0.047 2361 Dihedral : 7.611 73.423 1960 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.73 % Allowed : 21.39 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.21), residues: 1662 helix: 1.45 (0.16), residues: 966 sheet: -1.50 (0.55), residues: 61 loop : -0.77 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 203 HIS 0.017 0.001 HIS C 150 PHE 0.026 0.002 PHE A 629 TYR 0.021 0.001 TYR A 746 ARG 0.009 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 750) hydrogen bonds : angle 4.45752 ( 2178) covalent geometry : bond 0.00392 (13998) covalent geometry : angle 0.56028 (18946) ********************** 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 274 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8542 (mp) REVERT: A 459 SER cc_start: 0.9103 (t) cc_final: 0.8840 (t) REVERT: A 483 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.7815 (pp) REVERT: A 565 TYR cc_start: 0.8872 (t80) cc_final: 0.8373 (t80) REVERT: A 875 HIS cc_start: 0.7663 (OUTLIER) cc_final: 0.6798 (p90) REVERT: A 1058 MET cc_start: 0.8628 (mtm) cc_final: 0.8368 (mtm) REVERT: A 1135 GLU cc_start: 0.8532 (tt0) cc_final: 0.8159 (tt0) REVERT: A 1309 MET cc_start: 0.7626 (mmt) cc_final: 0.7333 (mmt) REVERT: A 1422 MET cc_start: 0.7451 (ptt) cc_final: 0.7042 (ptt) REVERT: B 134 ARG cc_start: 0.7476 (ptm160) cc_final: 0.6660 (mtp-110) REVERT: B 152 LEU cc_start: 0.9184 (tp) cc_final: 0.8789 (tt) REVERT: D 131 ILE cc_start: 0.6221 (mp) cc_final: 0.5833 (mp) REVERT: E 136 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7133 (t0) outliers start: 42 outliers final: 30 residues processed: 257 average time/residue: 0.2468 time to fit residues: 96.5436 Evaluate side-chains 253 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 295 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 487 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 600 CYS Chi-restraints excluded: chain A residue 614 VAL 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 847 GLU 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 971 ILE Chi-restraints excluded: chain A residue 1072 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 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 135 LEU Chi-restraints excluded: chain E residue 136 ASP 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 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 74 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS A 874 GLN ** 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 = 0.3479 r_free = 0.3479 target = 0.119140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099188 restraints weight = 25290.699| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.12 r_work: 0.3067 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13998 Z= 0.151 Angle : 0.564 8.367 18946 Z= 0.297 Chirality : 0.042 0.266 2201 Planarity : 0.004 0.048 2361 Dihedral : 7.600 73.408 1960 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.60 % Allowed : 21.26 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.21), residues: 1662 helix: 1.45 (0.16), residues: 972 sheet: -1.39 (0.55), residues: 61 loop : -0.80 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 203 HIS 0.017 0.001 HIS C 150 PHE 0.026 0.002 PHE A 629 TYR 0.019 0.001 TYR A 746 ARG 0.009 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 750) hydrogen bonds : angle 4.43923 ( 2178) covalent geometry : bond 0.00352 (13998) covalent geometry : angle 0.56438 (18946) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6042.09 seconds wall clock time: 106 minutes 13.73 seconds (6373.73 seconds total)